Open-access and free articles in Journal of Applied Crystallographyhttp://journals.iucr.org/j/journalhomepage.html
Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.en-gbCopyright (c) 2016 International Union of CrystallographyInternational Union of CrystallographyInternational Union of Crystallographyhttp://journals.iucr.orgurn:issn:0021-8898Journal of Applied Crystallography covers a wide range of crystallographic topics from the viewpoints of both techniques and theory. The journal presents articles on the application of crystallographic techniques and on the related apparatus and computer software. For many years, Journal of Applied Crystallography has been the main vehicle for the publication of small-angle scattering articles and powder diffraction techniques. The journal is the primary place where crystallographic computer program information is published.text/htmlOpen-access and free articles in Journal of Applied Crystallographytextyearly62002-02-01T00:00+00:00med@iucr.orgJournal of Applied CrystallographyCopyright (c) 2016 International Union of Crystallographyurn:issn:0021-8898

Open-access and free articles in Journal of Applied Crystallographyhttp://journals.iucr.org/logos/rss10j.gifhttp://journals.iucr.org/j/journalhomepage.html
Still imageUse of small-angle X-ray scattering to resolve intracellular structure changes of Escherichia coli cells induced by antibiotic treatmentThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16 th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?jk5008
The application of small-angle X-ray scattering (SAXS) to whole Escherichia coli cells is challenging owing to the variety of internal constituents. To resolve their contributions, the outer shape was captured by ultra-small-angle X-ray scattering and combined with the internal structure resolved by SAXS. Building on these data, a model for the major structural components of E. coli was developed. It was possible to deduce information on the occupied volume, occurrence and average size of the most important intracellular constituents: ribosomes, DNA and proteins. E. coli was studied after treatment with three different antibiotic agents (chloramphenicol, tetracycline and rifampicin) and the impact on the intracellular constituents was monitored.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Gundlach, A.R. vonGaramus, V.M.Willey, T.M.Ilavsky, J.Hilpert, K.Rosenhahn, A.2016-12-01doi:10.1107/S1600576716018562International Union of CrystallographyA combination of small- and ultra-small-angle X-ray scattering enabled the resolution of important intracellular constituents in Escherichia coli (ribosomes, DNA and proteins). The impact of treatment with three antibiotic agents was monitored.enESCHERICHIA COLI ULTRASTRUCTURE; ANTIBIOTICS; SMALL-ANGLE X-RAY SCATTERING; SAXS; ULTRA-SMALL-ANGLE X-RAY SCATTERING; USAXS; TRANSMISSION ELECTRON MICROSCOPY; TEMThe application of small-angle X-ray scattering (SAXS) to whole Escherichia coli cells is challenging owing to the variety of internal constituents. To resolve their contributions, the outer shape was captured by ultra-small-angle X-ray scattering and combined with the internal structure resolved by SAXS. Building on these data, a model for the major structural components of E. coli was developed. It was possible to deduce information on the occupied volume, occurrence and average size of the most important intracellular constituents: ribosomes, DNA and proteins. E. coli was studied after treatment with three different antibiotic agents (chloramphenicol, tetracycline and rifampicin) and the impact on the intracellular constituents was monitored.text/htmlUse of small-angle X-ray scattering to resolve intracellular structure changes of Escherichia coli cells induced by antibiotic treatmentThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16 th International Conference on Small-Angle Scattering (SAS2015).text496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-12-012210research papers1600-5767December 2016med@iucr.org22161600-5767Structure beyond pair correlations: X-ray cross-correlation from colloidal crystalsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?zg5001
The results of an X-ray cross-correlation analysis (XCCA) study on hard-sphere colloidal crystals and glasses are presented. The article shows that cross-correlation functions can be used to extract structural information beyond the static structure factor in such systems. In particular, the powder average can be overcome by accessing the crystals' unit-cell structure. In this case, the results suggest that the crystal is of face-centered cubic type. It is demonstrated that XCCA is a valuable tool for X-ray crystallography, in particular for studies on colloidal systems. These are typically characterized by a rather poor crystalline quality due to size polydispersity and limitations in experimental resolution because of the small q values probed. Furthermore, nontrivial correlations are observed that allow a more detailed insight into crystal structures beyond conventional crystallography, especially to extend knowledge in structure formation processes and phase transitions.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Lehmkühler, F.Fischer, B.Müller, L.Ruta, B.Grübel, G.2016-11-08doi:10.1107/S1600576716017313International Union of CrystallographyAn X-ray cross-correlation study with emphasis on colloidal crystals is presented and demonstrates how to access higher-order structure beyond pair correlations. In this way symmetries of the crystal can be determined that are inaccessible in conventional crystallography.enCOLLOIDAL CRYSTALS; COHERENT X-RAY SCATTERING; SMALL-ANGLE X-RAY SCATTERING; X-RAY CROSS-CORRELATION ANALYSISThe results of an X-ray cross-correlation analysis (XCCA) study on hard-sphere colloidal crystals and glasses are presented. The article shows that cross-correlation functions can be used to extract structural information beyond the static structure factor in such systems. In particular, the powder average can be overcome by accessing the crystals' unit-cell structure. In this case, the results suggest that the crystal is of face-centered cubic type. It is demonstrated that XCCA is a valuable tool for X-ray crystallography, in particular for studies on colloidal systems. These are typically characterized by a rather poor crystalline quality due to size polydispersity and limitations in experimental resolution because of the small q values probed. Furthermore, nontrivial correlations are observed that allow a more detailed insight into crystal structures beyond conventional crystallography, especially to extend knowledge in structure formation processes and phase transitions.text/htmlStructure beyond pair correlations: X-ray cross-correlation from colloidal crystalsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-11-082046research papers1600-5767December 2016med@iucr.org20521600-5767Combinatorial refinement of thin-film microstructure, properties and process conditions: iterative nanoscale search for self-assembled TiAlN nanolamellaehttp://scripts.iucr.org/cgi-bin/paper?nb5185
Because of the tremendous variability of crystallite sizes and shapes in nano­materials, it is challenging to assess the corresponding size–property relationships and to identify microstructures with particular physical properties or even optimized functions. This task is especially difficult for nanomaterials formed by self-organization, where the spontaneous evolution of microstructure and properties is coupled. In this work, two compositionally graded TiAlN films were (i) grown using chemical vapour deposition by applying a varying ratio of reacting gases and (ii) subsequently analysed using cross-sectional synchrotron X-ray nanodiffraction, electron microscopy and nanoindentation in order to evaluate the microstructure and hardness depth gradients. The results indicate the formation of self-organized hexagonal–cubic and cubic–cubic nanolamellae with varying compositions and thicknesses in the range of ∼3–15 nm across the film thicknesses, depending on the actual composition of the reactive gas mixtures. On the basis of the occurrence of the nanolamellae and their correlation with the local film hardness, progressively narrower ranges of the composition and hardness were refined in three steps. The third film was produced using an AlCl3/TiCl4 precursor ratio of ∼1.9, resulting in the formation of an optimized lamellar microstructure with ∼1.3 nm thick cubic Ti(Al)N and ∼12 nm thick cubic Al(Ti)N nanolamellae which exhibits a maximal hardness of ∼36 GPa and an indentation modulus of ∼522 GPa. The presented approach of an iterative nanoscale search based on the application of cross-sectional synchrotron X-ray nanodiffraction and cross-sectional nanoindentation allows one to refine the relationship between (i) varying deposition conditions, (ii) gradients of microstructure and (iii) gradients of mechanical properties in nanostructured materials prepared as thin films. This is done in a combinatorial way in order to screen a wide range of deposition conditions, while identifying those that result in the formation of a particular microstructure with optimized functional attributes.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Zalesak, J.Todt, J.Pitonak, R.Köpf, A.Weißenbacher, R.Sartory, B.Burghammer, M.Daniel, R.Keckes, J.2016-12-01doi:10.1107/S1600576716017258International Union of CrystallographyA novel iterative combinatorial nanoscale search based on the application of cross-sectional synchrotron X-ray nanodiffraction and cross-sectional nanoindentation is used to refine the relationship between deposition conditions, microstructure and properties of nanostructured TiAlN thin films. Using three iterative steps, a nanolamellar TiAlN thin film with a maximal hardness of ∼36 GPa is developed.enX-RAY NANODIFFRACTION; THIN FILMS; NANOMATERIALS; COMBINATORIAL SEARCHBecause of the tremendous variability of crystallite sizes and shapes in nano­materials, it is challenging to assess the corresponding size–property relationships and to identify microstructures with particular physical properties or even optimized functions. This task is especially difficult for nanomaterials formed by self-organization, where the spontaneous evolution of microstructure and properties is coupled. In this work, two compositionally graded TiAlN films were (i) grown using chemical vapour deposition by applying a varying ratio of reacting gases and (ii) subsequently analysed using cross-sectional synchrotron X-ray nanodiffraction, electron microscopy and nanoindentation in order to evaluate the microstructure and hardness depth gradients. The results indicate the formation of self-organized hexagonal–cubic and cubic–cubic nanolamellae with varying compositions and thicknesses in the range of ∼3–15 nm across the film thicknesses, depending on the actual composition of the reactive gas mixtures. On the basis of the occurrence of the nanolamellae and their correlation with the local film hardness, progressively narrower ranges of the composition and hardness were refined in three steps. The third film was produced using an AlCl3/TiCl4 precursor ratio of ∼1.9, resulting in the formation of an optimized lamellar microstructure with ∼1.3 nm thick cubic Ti(Al)N and ∼12 nm thick cubic Al(Ti)N nanolamellae which exhibits a maximal hardness of ∼36 GPa and an indentation modulus of ∼522 GPa. The presented approach of an iterative nanoscale search based on the application of cross-sectional synchrotron X-ray nanodiffraction and cross-sectional nanoindentation allows one to refine the relationship between (i) varying deposition conditions, (ii) gradients of microstructure and (iii) gradients of mechanical properties in nanostructured materials prepared as thin films. This is done in a combinatorial way in order to screen a wide range of deposition conditions, while identifying those that result in the formation of a particular microstructure with optimized functional attributes.text/htmlCombinatorial refinement of thin-film microstructure, properties and process conditions: iterative nanoscale search for self-assembled TiAlN nanolamellaetext496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-12-012217research papers1600-5767December 2016med@iucr.org22251600-5767Synchrotron-based macromolecular crystallography module for an undergraduate biochemistry laboratory coursehttp://scripts.iucr.org/cgi-bin/paper?gj5166
This paper describes the introduction of synchrotron-based macromolecular crystallography (MX) into an undergraduate laboratory class. An introductory 2 week experimental module on MX, consisting of four laboratory sessions and two classroom lectures, was incorporated into a senior-level biochemistry class focused on a survey of biochemical techniques, including the experimental characterization of proteins. Students purified recombinant protein samples, set up crystallization plates and flash-cooled crystals for shipping to a synchrotron. Students then collected X-ray diffraction data sets from their crystals via the remote interface of the Molecular Biology Consortium beamline (4.2.2) at the Advanced Light Source in Berkeley, CA, USA. Processed diffraction data sets were transferred back to the laboratory and used in conjunction with partial protein models provided to the students for refinement and model building. The laboratory component was supplemented by up to 2 h of lectures by faculty with expertise in MX. This module can be easily adapted for implementation into other similar undergraduate classes, assuming the availability of local crystallographic expertise and access to remote data collection at a synchrotron source.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Stiers, K.M.Lee, C.B.Nix, J.C.Tanner, J.J.Beamer, L.J.2016-11-24doi:10.1107/S1600576716016800International Union of CrystallographyA 2 week module on macromolecular crystallography was introduced into an undergraduate biochemistry class, including the use of remote data collection at a synchrotron X-ray source.enUNDERGRADUATE EDUCATION; MACROMOLECULAR CRYSTALLOGRAPHY; SYNCHROTRON SOURCES; REMOTE DATA COLLECTIONThis paper describes the introduction of synchrotron-based macromolecular crystallography (MX) into an undergraduate laboratory class. An introductory 2 week experimental module on MX, consisting of four laboratory sessions and two classroom lectures, was incorporated into a senior-level biochemistry class focused on a survey of biochemical techniques, including the experimental characterization of proteins. Students purified recombinant protein samples, set up crystallization plates and flash-cooled crystals for shipping to a synchrotron. Students then collected X-ray diffraction data sets from their crystals via the remote interface of the Molecular Biology Consortium beamline (4.2.2) at the Advanced Light Source in Berkeley, CA, USA. Processed diffraction data sets were transferred back to the laboratory and used in conjunction with partial protein models provided to the students for refinement and model building. The laboratory component was supplemented by up to 2 h of lectures by faculty with expertise in MX. This module can be easily adapted for implementation into other similar undergraduate classes, assuming the availability of local crystallographic expertise and access to remote data collection at a synchrotron source.text/htmlSynchrotron-based macromolecular crystallography module for an undergraduate biochemistry laboratory coursetext496Copyright (c) 2016 International Union of CrystallographyJournal of Applied Crystallography2016-11-242235teaching and education1600-5767December 2016med@iucr.org22431600-5767SEC-SANS: size exclusion chromatography combined in situ with small-angle neutron scatteringThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?zg5006
The first implementation and use of an in situ size exclusion chromatography (SEC) system on a small-angle neutron scattering instrument (SANS) is described. The possibility of deploying such a system for biological solution scattering at the Institut Laue–Langevin (ILL) has arisen from the fact that current day SANS instruments at ILL now allow datasets to be acquired using small sample volumes with exposure times that are often shorter than a minute. This capability is of particular importance for the study of unstable biological macromolecules where aggregation or denaturation issues are a major problem. The first use of SEC-SANS on ILL's instrument D22 is described for a variety of proteins including one particularly aggregation-prone system.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Jordan, A.Jacques, M.Merrick, C.Devos, J.Forsyth, V.T.Porcar, L.Martel, A.2016-11-02doi:10.1107/S1600576716016514International Union of CrystallographyThis publication describes the combination of size exclusion chromatography with small-angle neutron scattering in situ. The need for this technique and the progress achieved thanks to it are illustrated by relevant examples.enSEC-SANS; SIZE EXCLUSION CHROMATOGRAPHY; SMALL-ANGLE NEUTRON SCATTERING; IN SITU; SAMPLE ENVIRONMENTThe first implementation and use of an in situ size exclusion chromatography (SEC) system on a small-angle neutron scattering instrument (SANS) is described. The possibility of deploying such a system for biological solution scattering at the Institut Laue–Langevin (ILL) has arisen from the fact that current day SANS instruments at ILL now allow datasets to be acquired using small sample volumes with exposure times that are often shorter than a minute. This capability is of particular importance for the study of unstable biological macromolecules where aggregation or denaturation issues are a major problem. The first use of SEC-SANS on ILL's instrument D22 is described for a variety of proteins including one particularly aggregation-prone system.text/htmlSEC-SANS: size exclusion chromatography combined in situ with small-angle neutron scatteringThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-11-022015research papers1600-5767December 2016med@iucr.org20201600-5767Contrast variation by dynamic nuclear polarization and time-of-flight small-angle neutron scattering. I. Application to industrial multi-component nanocompositesThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?zg5004
Dynamic nuclear polarization (DNP) at low temperature (1.2 K) and high magnetic field (3.3 T) was applied to a contrast variation study in small-angle neutron scattering (SANS) focusing on industrial rubber materials. By varying the scattering contrast by DNP, time-of-flight SANS profiles were obtained at the pulsed neutron source of the Japan Proton Accelerator Research Complex (J-PARC). The concentration of a small organic molecule, (2,2,6,6-tetramethylpiperidine-1-yl)oxy (TEMPO), was carefully controlled by a doping method using vapour sorption into the rubber specimens. With the assistance of microwave irradiation (94 GHz), almost full polarization of the paramagnetic electronic spin of TEMPO was transferred to the spin state of hydrogen (protons) in the rubber materials to obtain a high proton spin polarization (PH). The following samples were prepared: (i) a binary mixture of styrene–butadiene random copolymer (SBR) with silica particles (SBR/SP); and (ii) a ternary mixture of SBR with silica and carbon black particles (SBR/SP/CP). For the binary mixture (SBR/SP), the intensity of SANS significantly increased or decreased while keeping its q dependence for PH = −35% or PH = 40%, respectively. The q behaviour of SANS for the SBR/SP mixture can be reproduced using the form factor of a spherical particle. The intensity at low q (∼0.01 Å−1) varied as a quadratic function of PH and indicated a minimum value at PH = 30%, which can be explained by the scattering contrast between SP and SBR. The scattering intensity at high q (∼0.3 Å−1) decreased with increasing PH, which is attributed to the incoherent scattering from hydrogen. For the ternary mixture (SBR/SP/CP), the q behaviour of SANS was varied by changing PH. At PH = −35%, the scattering maxima originating from the form factor of SP prevailed, whereas at PH = 29% and PH = 38%, the scattering maxima disappeared. After decomposition of the total SANS according to inverse matrix calculations, the partial scattering functions were obtained. The partial scattering function obtained for SP was well reproduced by a spherical form factor and matched the SANS profile for the SBR/SP mixture. The partial scattering function for CP exhibited surface fractal behaviour according to q−3.6, which is consistent with the results for the SBR/CP mixture.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Noda, Y.Koizumi, S.Masui, T.Mashita, R.Kishimoto, H.Yamaguchi, D.Kumada, T.Takata, S.-Ohishi, K.Suzuki, J.-2016-11-08doi:10.1107/S1600576716016472International Union of CrystallographyContrast variation small-angle neutron scattering by dynamic nuclear polarization is applied to industrial multi-component nanocomposites.enSMALL-ANGLE NEUTRON SCATTERING (SANS); CONTRAST VARIATION; DYNAMIC NUCLEAR POLARIZATION; TERNARY MIXTURES; NANOCOMPOSITESDynamic nuclear polarization (DNP) at low temperature (1.2 K) and high magnetic field (3.3 T) was applied to a contrast variation study in small-angle neutron scattering (SANS) focusing on industrial rubber materials. By varying the scattering contrast by DNP, time-of-flight SANS profiles were obtained at the pulsed neutron source of the Japan Proton Accelerator Research Complex (J-PARC). The concentration of a small organic molecule, (2,2,6,6-tetramethylpiperidine-1-yl)oxy (TEMPO), was carefully controlled by a doping method using vapour sorption into the rubber specimens. With the assistance of microwave irradiation (94 GHz), almost full polarization of the paramagnetic electronic spin of TEMPO was transferred to the spin state of hydrogen (protons) in the rubber materials to obtain a high proton spin polarization (PH). The following samples were prepared: (i) a binary mixture of styrene–butadiene random copolymer (SBR) with silica particles (SBR/SP); and (ii) a ternary mixture of SBR with silica and carbon black particles (SBR/SP/CP). For the binary mixture (SBR/SP), the intensity of SANS significantly increased or decreased while keeping its q dependence for PH = −35% or PH = 40%, respectively. The q behaviour of SANS for the SBR/SP mixture can be reproduced using the form factor of a spherical particle. The intensity at low q (∼0.01 Å−1) varied as a quadratic function of PH and indicated a minimum value at PH = 30%, which can be explained by the scattering contrast between SP and SBR. The scattering intensity at high q (∼0.3 Å−1) decreased with increasing PH, which is attributed to the incoherent scattering from hydrogen. For the ternary mixture (SBR/SP/CP), the q behaviour of SANS was varied by changing PH. At PH = −35%, the scattering maxima originating from the form factor of SP prevailed, whereas at PH = 29% and PH = 38%, the scattering maxima disappeared. After decomposition of the total SANS according to inverse matrix calculations, the partial scattering functions were obtained. The partial scattering function obtained for SP was well reproduced by a spherical form factor and matched the SANS profile for the SBR/SP mixture. The partial scattering function for CP exhibited surface fractal behaviour according to q−3.6, which is consistent with the results for the SBR/CP mixture.text/htmlContrast variation by dynamic nuclear polarization and time-of-flight small-angle neutron scattering. I. Application to industrial multi-component nanocompositesThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-11-082036research papers1600-5767December 2016med@iucr.org20451600-5767Pushing the limits of crystallographyhttp://scripts.iucr.org/cgi-bin/paper?to5146
A very serious concern of scientists dealing with crystal structure refinement, including theoretical research, pertains to the characteristic bias in calculated versus measured diffraction intensities, observed particularly in the weak reflection regime. This bias is here attributed to corrective factors for phonons and, even more distinctly, phasons, and credible proof supporting this assumption is given. The lack of a consistent theory of phasons in quasicrystals significantly contributes to this characteristic bias. It is shown that the most commonly used exponential Debye–Waller factor for phasons fails in the case of quasicrystals, and a novel method of calculating the correction factor within a statistical approach is proposed. The results obtained for model quasiperiodic systems show that phasonic perturbations can be successfully described and refinement fits of high quality are achievable. The standard Debye–Waller factor for phonons works equally well for periodic and quasiperiodic crystals, and it is only in the last steps of a refinement that different correction functions need to be applied to improve the fit quality.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Wolny, J.Buganski, I.Kuczera, P.Strzalka, R.2016-11-18doi:10.1107/S160057671601637XInternational Union of CrystallographyA statistical method is discussed, which solves the problem of bias in fitted versus observed diffraction intensities for quasicrystals.enDEBYE-WALLER CORRECTION; PHASONS; QUASICRYSTALS; STATISTICAL METHODS; AVERAGE UNIT CELLA very serious concern of scientists dealing with crystal structure refinement, including theoretical research, pertains to the characteristic bias in calculated versus measured diffraction intensities, observed particularly in the weak reflection regime. This bias is here attributed to corrective factors for phonons and, even more distinctly, phasons, and credible proof supporting this assumption is given. The lack of a consistent theory of phasons in quasicrystals significantly contributes to this characteristic bias. It is shown that the most commonly used exponential Debye–Waller factor for phasons fails in the case of quasicrystals, and a novel method of calculating the correction factor within a statistical approach is proposed. The results obtained for model quasiperiodic systems show that phasonic perturbations can be successfully described and refinement fits of high quality are achievable. The standard Debye–Waller factor for phonons works equally well for periodic and quasiperiodic crystals, and it is only in the last steps of a refinement that different correction functions need to be applied to improve the fit quality.text/htmlPushing the limits of crystallographytext496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-11-182106research papers1600-5767December 2016med@iucr.org21151600-5767Small-angle scattering and morphologies of ultra-flexible microemulsionsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?zg5005
The phase diagrams of ternary mixtures of partly miscible solvents containing a hydrotropic co-solvent exhibit a variable miscibility gap and one critical point. This work investigates the entire monophasic region far from and near to the miscibility gap in octan-1-ol/ethanol/water, for which ultra-flexible micro­emulsions (UFMEs) are observed by small-angle scattering techniques. SWAXS (combined small- and wide-angle X-ray scattering) allows the elucidation of these types of structure. Three distinct areas can be identified in the phase diagram, with scattering data resembling those from direct, bicontinuous and reverse local structures. These UFMEs are far more polydisperse than their surfactant-based counterparts. Water-rich and solvent-rich domains are only delimited by a small excess of hydrotrope, instead of a well defined surfactant layer of fixed area per molecule. It is shown that all scattering spectra obtained for the nanostructured compositions can be modelled by a simple unified analytical model composed of two uncorrelated contributions. The main one is the Ornstein–Zernike formula for composition fluctuations which gives information about the pseudo-phase domain size. The second is a Lorentzian that captures the structure of at least one of the coexisting pseudo-phases. No Porod law can be measured in the SAXS domain. The proposed expression gives access to two characteristic sizes as well as one inter-aggregate distance.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Prevost, S.Lopian, T.Pleines, M.Diat, O.Zemb, T.2016-11-11doi:10.1107/S1600576716016150International Union of CrystallographyThree-component fluids can exhibit structured density fluctuations, and their small-angle scattering patterns present similarities to those of classical microemulsions. One general analytical expression with two additive contributions (one for the two immiscible fluids and a smaller one for a structured fluid) allows the whole phase diagram to be mapped in the single-phase domain.enULTRA-FLEXIBLE MICROEMULSIONS; SURFACTANT-FREE MICROEMULSIONS; MESOSCALE SOLUBILIZATION; SMALL-ANGLE SCATTERING (SAS); TERNARY PHASE DIAGRAMSThe phase diagrams of ternary mixtures of partly miscible solvents containing a hydrotropic co-solvent exhibit a variable miscibility gap and one critical point. This work investigates the entire monophasic region far from and near to the miscibility gap in octan-1-ol/ethanol/water, for which ultra-flexible micro­emulsions (UFMEs) are observed by small-angle scattering techniques. SWAXS (combined small- and wide-angle X-ray scattering) allows the elucidation of these types of structure. Three distinct areas can be identified in the phase diagram, with scattering data resembling those from direct, bicontinuous and reverse local structures. These UFMEs are far more polydisperse than their surfactant-based counterparts. Water-rich and solvent-rich domains are only delimited by a small excess of hydrotrope, instead of a well defined surfactant layer of fixed area per molecule. It is shown that all scattering spectra obtained for the nanostructured compositions can be modelled by a simple unified analytical model composed of two uncorrelated contributions. The main one is the Ornstein–Zernike formula for composition fluctuations which gives information about the pseudo-phase domain size. The second is a Lorentzian that captures the structure of at least one of the coexisting pseudo-phases. No Porod law can be measured in the SAXS domain. The proposed expression gives access to two characteristic sizes as well as one inter-aggregate distance.text/htmlSmall-angle scattering and morphologies of ultra-flexible microemulsionsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-11-112063research papers1600-5767December 2016med@iucr.org20721600-5767Multiparameter characterization of subnanometre Cr/Sc multilayers based on complementary measurementshttp://scripts.iucr.org/cgi-bin/paper?vh5064
Cr/Sc multilayer systems can be used as near-normal incidence mirrors for the water window spectral range. It is shown that a detailed characterization of these multilayer systems with 400 bilayers of Cr and Sc, each with individual layer thicknesses <1 nm, is attainable by the combination of several analytical techniques. EUV and X-ray reflectance measurements, resonant EUV reflectance across the Sc L edge, and X-ray standing wave fluorescence measurements were used. The parameters of the multilayer model were determined via a particle-swarm optimizer and validated using a Markov chain Monte Carlo maximum-likelihood approach. For the determination of the interface roughness, diffuse scattering measurements were conducted.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Haase, A.Bajt, S.Hönicke, P.Soltwisch, V.Scholze, F.2016-11-24doi:10.1107/S1600576716015776International Union of CrystallographyThis paper reports the characterization of subnanometre Cr/Sc multilayers through the application of several analytical experiments. A combined analysis is shown and verified by Markov chain Monte Carlo sampling.enMULTILAYERS; WATER WINDOW; METROLOGY; ROUGHNESS; INTERDIFFUSIONCr/Sc multilayer systems can be used as near-normal incidence mirrors for the water window spectral range. It is shown that a detailed characterization of these multilayer systems with 400 bilayers of Cr and Sc, each with individual layer thicknesses <1 nm, is attainable by the combination of several analytical techniques. EUV and X-ray reflectance measurements, resonant EUV reflectance across the Sc L edge, and X-ray standing wave fluorescence measurements were used. The parameters of the multilayer model were determined via a particle-swarm optimizer and validated using a Markov chain Monte Carlo maximum-likelihood approach. For the determination of the interface roughness, diffuse scattering measurements were conducted.text/htmlMultiparameter characterization of subnanometre Cr/Sc multilayers based on complementary measurementstext496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-11-242161research papers1600-5767December 2016med@iucr.org21711600-5767Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)This article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?zg5003
The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Perkins, S.J.Wright, D.W.Zhang, H.Brookes, E.H.Chen, J.Irving, T.C.Krueger, S.Barlow, D.J.Edler, K.J.Scott, D.J.Terrill, N.J.King, S.M.Butler, P.D.Curtis, J.E.2016-10-14doi:10.1107/S160057671601517XInternational Union of CrystallographyThe CCP-SAS project is currently developing software for the atomistic and coarse-grained molecular modelling of X-ray and neutron small-angle scattering data. Its computational framework is described, alongside applications in biology and soft matter.enMOLECULAR DYNAMICS (MD); MOLECULAR MODELLING; SCATTERING CURVE FITS; SMALL-ANGLE-NEUTRON SCATTERING (SANS); SMALL-ANGLE-X-RAY SCATTERING (SAXS)The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web, and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.text/htmlAtomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)This article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-10-141861research papers1600-5767December 2016med@iucr.org18751600-5767ContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminantshttp://scripts.iucr.org/cgi-bin/paper?ei5009
Solving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for `crystallization and preliminary X-ray analysis' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hungler, A.Momin, A.Diederichs, K.Arold, S.T.2016-11-02doi:10.1107/S1600576716014965International Union of CrystallographyA webserver, titled ContaMiner, has been established, which allows fast molecular-replacement-based screening of crystallographic data against a database (ContaBase) of currently 62 potential contaminants. ContaMiner enables systematic screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for `crystallization and preliminary X-ray analysis' publications.enDIFFRACTION; MOLECULAR REPLACEMENT; CONTAMINANT CRYSTALS; COMPUTER PROGRAMSSolving the phase problem in protein X-ray crystallography relies heavily on the identity of the crystallized protein, especially when molecular replacement (MR) methods are used. Yet, it is not uncommon that a contaminant crystallizes instead of the protein of interest. Such contaminants may be proteins from the expression host organism, protein fusion tags or proteins added during the purification steps. Many contaminants co-purify easily, crystallize and give good diffraction data. Identification of contaminant crystals may take time, since the presence of the contaminant is unexpected and its identity unknown. A webserver (ContaMiner) and a contaminant database (ContaBase) have been established, to allow fast MR-based screening of crystallographic data against currently 62 known contaminants. The web-based ContaMiner (available at http://strube.cbrc.kaust.edu.sa/contaminer/) currently produces results in 5 min to 4 h. The program is also available in a github repository and can be installed locally. ContaMiner enables screening of novel crystals at synchrotron beamlines, and it would be valuable as a routine safety check for `crystallization and preliminary X-ray analysis' publications. Thus, in addition to potentially saving X-ray crystallographers much time and effort, ContaMiner might considerably lower the risk of publishing erroneous data.text/htmlContaMiner and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminantstext496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-11-022252computer programs1600-5767December 2016med@iucr.org22581600-5767A synchrotron X-ray diffraction deconvolution method for the measurement of residual stress in thermal barrier coatings as a function of depthhttp://scripts.iucr.org/cgi-bin/paper?kc5041
The average residual stress distribution as a function of depth in an air plasma-sprayed yttria stabilized zirconia top coat used in thermal barrier coating (TBC) systems was measured using synchrotron radiation X-ray diffraction in reflection geometry on station I15 at Diamond Light Source, UK, employing a series of incidence angles. The stress values were calculated from data deconvoluted from diffraction patterns collected at increasing depths. The stress was found to be compressive through the thickness of the TBC and a fluctuation in the trend of the stress profile was indicated in some samples. Typically this fluctuation was observed to increase from the surface to the middle of the coating, decrease a little and then increase again towards the interface. The stress at the interface region was observed to be around 300 MPa, which agrees well with the reported values. The trend of the observed residual stress was found to be related to the crack distribution in the samples, in particular a large crack propagating from the middle of the coating. The method shows promise for the development of a nondestructive test for as-manufactured samples.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Li, C.Jacques, S.D.M.Chen, Y.Daisenberger, D.Xiao, P.Markocsan, N.Nylen, P.Cernik, R.J.2016-10-21doi:10.1107/S1600576716013935International Union of CrystallographyThe strain profile in a YZrO3 thermal barrier coating has been measured and shows possible mechanisms of in-service failure. The method relies on deconvoluting diffraction patterns at different depths for the reflection geometry used. The nondestructive test could be applied to whole fabricated componentsenTHERMAL BARRIER COATINGS; SYNCHROTRON GLANCING-ANGLE X-RAY DIFFRACTION; STRESS MAPPING; FLAT PLATE POWDER DIFFRACTIONThe average residual stress distribution as a function of depth in an air plasma-sprayed yttria stabilized zirconia top coat used in thermal barrier coating (TBC) systems was measured using synchrotron radiation X-ray diffraction in reflection geometry on station I15 at Diamond Light Source, UK, employing a series of incidence angles. The stress values were calculated from data deconvoluted from diffraction patterns collected at increasing depths. The stress was found to be compressive through the thickness of the TBC and a fluctuation in the trend of the stress profile was indicated in some samples. Typically this fluctuation was observed to increase from the surface to the middle of the coating, decrease a little and then increase again towards the interface. The stress at the interface region was observed to be around 300 MPa, which agrees well with the reported values. The trend of the observed residual stress was found to be related to the crack distribution in the samples, in particular a large crack propagating from the middle of the coating. The method shows promise for the development of a nondestructive test for as-manufactured samples.text/htmlA synchrotron X-ray diffraction deconvolution method for the measurement of residual stress in thermal barrier coatings as a function of depthtext496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-10-211904research papers1600-5767December 2016med@iucr.org19111600-5767Pore shape and sorption behaviour in mesoporous ordered silica filmsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?aj5278
Mesoporous silica films templated by pluronic P123 were prepared using spin and dip coating. The ordered cylindrical structure within the films deforms due to shrinkage during calcination. Grazing-incidence small-angle X-ray scattering (GISAXS) measurements reveal that both the unit cell and the cross section of the pores decrease in size, mainly normal to the surface of the substrate, leading to elliptical cross sections of the pores with axis ratios of about 1:2. Water take-up by the pores upon changing the relative humidity can be monitored quantitatively by the shift in the critical angle of X-ray reflection as seen by the Yoneda peak.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Fritz-Popovski, G.Morak, R.Sharifi, P.Amenitsch, H.Paris, O.2016-09-23doi:10.1107/S1600576716013698International Union of CrystallographyThe shape and sorption behaviour of pores in mesoporous ordered silica films are determined from grazing-incidence small-angle X-ray scattering data.enSORPTION BEHAVIOUR; PORE SHAPE; MESOPOROUS SILICA FILMS; GRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING; GISAXS; SPIN COATING; DIP COATINGMesoporous silica films templated by pluronic P123 were prepared using spin and dip coating. The ordered cylindrical structure within the films deforms due to shrinkage during calcination. Grazing-incidence small-angle X-ray scattering (GISAXS) measurements reveal that both the unit cell and the cross section of the pores decrease in size, mainly normal to the surface of the substrate, leading to elliptical cross sections of the pores with axis ratios of about 1:2. Water take-up by the pores upon changing the relative humidity can be monitored quantitatively by the shift in the critical angle of X-ray reflection as seen by the Yoneda peak.text/htmlPore shape and sorption behaviour in mesoporous ordered silica filmsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-09-231713research papers1600-5767October 2016med@iucr.org17201600-5767Formation of swift heavy ion tracks on a rutile TiO2 (001) surfaceThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?aj5279
Nanostructuring of surfaces and two-dimensional materials using swift heavy ions offers some unique possibilities owing to the deposition of a large amount of energy localized within a nanoscale volume surrounding the ion trajectory. To fully exploit this feature, the morphology of nanostructures formed after ion impact has to be known in detail. In the present work the response of a rutile TiO2 (001) surface to grazing-incidence swift heavy ion irradiation is investigated. Surface ion tracks with the well known intermittent inner structure were successfully produced using 23 MeV I ions. Samples irradiated with different ion fluences were investigated using atomic force microscopy and grazing-incidence small-angle X-ray scattering. With these two complementary approaches, a detailed description of the swift heavy ion impact sites, i.e. the ion tracks on the surface, can be obtained even for the case of multiple ion track overlap. In addition to the structural investigation of surface ion tracks, the change in stoichiometry of the rutile TiO2 (001) surface during swift heavy ion irradiation was monitored using in situ time-of-flight elastic recoil detection analysis, and a preferential loss of oxygen was found.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Karlušić, M.Bernstorff, S.Siketić, Z.Šantić, B.Bogdanović-Radović, I.Jakšić, M.Schleberger, M.Buljan, M.2016-09-23doi:10.1107/S1600576716013704International Union of CrystallographyFormation of ion tracks on a rutile TiO2 (001) surface after exposure to swift heavy ions under grazing incidence is studied using atomic force microscopy, grazing-incidence small-angle X-ray scattering and in situ time-of-flight elastic recoil detection analysis.enSWIFT HEAVY IONS; ION TRACKS; TIO2; RUTILE; GRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING; GISAXS; ATOMIC FORCE MICROSCOPY; ELASTIC RECOIL DETECTION ANALYSISNanostructuring of surfaces and two-dimensional materials using swift heavy ions offers some unique possibilities owing to the deposition of a large amount of energy localized within a nanoscale volume surrounding the ion trajectory. To fully exploit this feature, the morphology of nanostructures formed after ion impact has to be known in detail. In the present work the response of a rutile TiO2 (001) surface to grazing-incidence swift heavy ion irradiation is investigated. Surface ion tracks with the well known intermittent inner structure were successfully produced using 23 MeV I ions. Samples irradiated with different ion fluences were investigated using atomic force microscopy and grazing-incidence small-angle X-ray scattering. With these two complementary approaches, a detailed description of the swift heavy ion impact sites, i.e. the ion tracks on the surface, can be obtained even for the case of multiple ion track overlap. In addition to the structural investigation of surface ion tracks, the change in stoichiometry of the rutile TiO2 (001) surface during swift heavy ion irradiation was monitored using in situ time-of-flight elastic recoil detection analysis, and a preferential loss of oxygen was found.text/htmlFormation of swift heavy ion tracks on a rutile TiO2 (001) surfaceThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-09-231704research papers1600-5767October 2016med@iucr.org17121600-5767Robust background modelling in DIALShttp://scripts.iucr.org/cgi-bin/paper?ap5008
A method for estimating the background under each reflection during integration that is robust in the presence of pixel outliers is presented. The method uses a generalized linear model approach that is more appropriate for use with Poisson distributed data than traditional approaches to pixel outlier handling in integration programs. The algorithm is most applicable to data with a very low background level where assumptions of a normal distribution are no longer valid as an approximation to the Poisson distribution. It is shown that traditional methods can result in the systematic underestimation of background values. This then results in the reflection intensities being overestimated and gives rise to a change in the overall distribution of reflection intensities in a dataset such that too few weak reflections appear to be recorded. Statistical tests performed during data reduction may mistakenly attribute this to merohedral twinning in the crystal. Application of the robust generalized linear model algorithm is shown to correct for this bias.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Parkhurst, J.M.Winter, G.Waterman, D.G.Fuentes-Montero, L.Gildea, R.J.Murshudov, G.N.Evans, G.2016-10-21doi:10.1107/S1600576716013595International Union of CrystallographyThe application of a robust generalized linear model framework for the modelling of reflection backgrounds in X-ray diffraction images is described.enINTEGRATION; ROBUST OUTLIER REJECTION; GENERALIZED LINEAR MODELS; BACKGROUND MODELLINGA method for estimating the background under each reflection during integration that is robust in the presence of pixel outliers is presented. The method uses a generalized linear model approach that is more appropriate for use with Poisson distributed data than traditional approaches to pixel outlier handling in integration programs. The algorithm is most applicable to data with a very low background level where assumptions of a normal distribution are no longer valid as an approximation to the Poisson distribution. It is shown that traditional methods can result in the systematic underestimation of background values. This then results in the reflection intensities being overestimated and gives rise to a change in the overall distribution of reflection intensities in a dataset such that too few weak reflections appear to be recorded. Statistical tests performed during data reduction may mistakenly attribute this to merohedral twinning in the crystal. Application of the robust generalized linear model algorithm is shown to correct for this bias.text/htmlRobust background modelling in DIALStext496http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-10-211912research papers1600-5767December 2016med@iucr.org19211600-5767Magnetic scattering in the simultaneous measurement of small-angle neutron scattering and Bragg edge transmission from steelThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?jk5010
Pulsed neutron sources enable the simultaneous measurement of small-angle neutron scattering (SANS) and Bragg edge transmission. This simultaneous measurement is useful for microstructural characterization in steel. Since most steels are ferromagnetic, magnetic scattering contributions should be considered in both SANS and Bragg edge transmission analyses. An expression for the magnetic scattering contribution to Bragg edge transmission analysis has been derived. The analysis using this expression was applied to Cu steel. The ferrite crystallite size estimated from this Bragg edge transmission analysis with the magnetic scattering contribution was larger than that estimated using conventional expressions. This result indicates that magnetic scattering has to be taken into account for quantitative Bragg edge transmission analysis. In the SANS analysis, the ratio of magnetic to nuclear scattering contributions revealed that the precipitates consist of body-centered cubic Cu0.7Fe0.3 and pure Cu, which probably has 9R structure including elastic strain and vacancies. These results show that effective use of the magnetic scattering contribution allows detailed analyses of steel microstructure.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Oba, Y.Morooka, S.Ohishi, K.Sato, N.Inoue, R.Adachi, N.Suzuki, J.Tsuchiyama, T.Gilbert, E.P.Sugiyama, M.2016-09-16doi:10.1107/S1600576716013133International Union of CrystallographyA technique for the analysis of magnetic scattering has been developed, where small-angle neutron scattering and Bragg edge transmission measurements are performed simultaneously. This technique is shown to provide crystallographic information for ferrite crystallites and nanostructural information for precipitates in steel.enSMALL-ANGLE NEUTRON SCATTERING; BRAGG EDGE TRANSMISSION; STEEL; MAGNETIC SCATTERINGPulsed neutron sources enable the simultaneous measurement of small-angle neutron scattering (SANS) and Bragg edge transmission. This simultaneous measurement is useful for microstructural characterization in steel. Since most steels are ferromagnetic, magnetic scattering contributions should be considered in both SANS and Bragg edge transmission analyses. An expression for the magnetic scattering contribution to Bragg edge transmission analysis has been derived. The analysis using this expression was applied to Cu steel. The ferrite crystallite size estimated from this Bragg edge transmission analysis with the magnetic scattering contribution was larger than that estimated using conventional expressions. This result indicates that magnetic scattering has to be taken into account for quantitative Bragg edge transmission analysis. In the SANS analysis, the ratio of magnetic to nuclear scattering contributions revealed that the precipitates consist of body-centered cubic Cu0.7Fe0.3 and pure Cu, which probably has 9R structure including elastic strain and vacancies. These results show that effective use of the magnetic scattering contribution allows detailed analyses of steel microstructure.text/htmlMagnetic scattering in the simultaneous measurement of small-angle neutron scattering and Bragg edge transmission from steelThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-09-161659research papers1600-5767October 2016med@iucr.org16641600-5767Phase-targeted X-ray diffractionhttp://scripts.iucr.org/cgi-bin/paper?nb5176
A powder X-ray diffraction (XRD) method to enhance the signal of a specific crystalline phase within a mixture is presented for the first time. Specificity to the targeted phase relies on finding coincidences in the ratios of crystal d spacings and the ratios of elemental characteristic X-ray energies. Such coincidences can be exploited so that the two crystal planes diffract through the same scattering angle at two different X-ray energies. An energy-resolving detector placed at the appropriate scattering angle will detect a significantly enhanced signal at these energies if the target mineral or phase is present in the sample. When implemented using high scattering angles, for example 2θ > 150°, the method is tolerant to sample morphology and distance on the scale of ∼2 mm. The principle of the method is demonstrated experimentally using Pd Lα1 and Pd Lβ1 emission lines to enhance the diffraction signal of quartz. Both a pure quartz powder pellet and an unprepared mudstone rock specimen are used to test and develop the phase-targeted method. The technique is further demonstrated in the sensitive detection of retained austenite in steel samples using a combination of In Lβ1 and Ti Kβ emission lines. For both these examples it is also shown how the use of an attenuating foil, with an absorption edge close to and above the higher-energy characteristic X-ray line, can serve to isolate to some degree the coincidence signals from other fluorescence and diffraction peaks in the detected spectrum. The phase-targeted XRD technique is suitable for implementation using low-cost off-the-shelf components in a handheld or in-line instrument format.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hansford, G.M.2016-09-01doi:10.1107/S1600576716011936International Union of CrystallographyA method to enhance the X-ray diffraction signal of a specific targeted crystalline phase within a sample is presented. This technique can be implemented in a handheld or in-line instrument format.enENERGY-DISPERSIVE X-RAY DIFFRACTION; PHASE SPECIFICITY; TARGET PHASES; HANDHELD INSTRUMENTATION; RETAINED AUSTENITE; IN-LINE INSTRUMENTATIONA powder X-ray diffraction (XRD) method to enhance the signal of a specific crystalline phase within a mixture is presented for the first time. Specificity to the targeted phase relies on finding coincidences in the ratios of crystal d spacings and the ratios of elemental characteristic X-ray energies. Such coincidences can be exploited so that the two crystal planes diffract through the same scattering angle at two different X-ray energies. An energy-resolving detector placed at the appropriate scattering angle will detect a significantly enhanced signal at these energies if the target mineral or phase is present in the sample. When implemented using high scattering angles, for example 2θ > 150°, the method is tolerant to sample morphology and distance on the scale of ∼2 mm. The principle of the method is demonstrated experimentally using Pd Lα1 and Pd Lβ1 emission lines to enhance the diffraction signal of quartz. Both a pure quartz powder pellet and an unprepared mudstone rock specimen are used to test and develop the phase-targeted method. The technique is further demonstrated in the sensitive detection of retained austenite in steel samples using a combination of In Lβ1 and Ti Kβ emission lines. For both these examples it is also shown how the use of an attenuating foil, with an absorption edge close to and above the higher-energy characteristic X-ray line, can serve to isolate to some degree the coincidence signals from other fluorescence and diffraction peaks in the detected spectrum. The phase-targeted XRD technique is suitable for implementation using low-cost off-the-shelf components in a handheld or in-line instrument format.text/htmlPhase-targeted X-ray diffractiontext495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-09-011561research papers1600-5767October 2016med@iucr.org15711600-5767The new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solutionThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?aj5277
The beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Li, N.Li, X.Wang, Y.Liu, G.Zhou, P.Wu, H.Hong, C.Bian, F.Zhang, R.2016-08-10doi:10.1107/S160057671601195XInternational Union of CrystallographyA new biological small-angle X-ray scattering beamline (BioSAXS, BL19U2) at the Shanghai Synchrotron Radiation Facility (SSRF) is dedicated exclusively to small-angle scattering experiments from biological macromolecules in solution. As part of the important facilities in the National Center for Protein Sciences Shanghai (NCPSS), this BioSAXS beamline is the first in China to serve the rapidly increasing biology communities.enBIOLOGICAL SMALL-ANGLE X-RAY SCATTERING; AUTOMATION AND HIGH BRILLIANCE; STRUCTURAL BIOLOGYThe beamline BL19U2 is located in the Shanghai Synchrotron Radiation Facility (SSRF) and is its first beamline dedicated to biological material small-angle X-ray scattering (BioSAXS). The electrons come from an undulator which can provide high brilliance for the BL19U2 end stations. A double flat silicon crystal (111) monochromator is used in BL19U2, with a tunable monochromatic photon energy ranging from 7 to 15 keV. To meet the rapidly growing demands of crystallographers, biochemists and structural biologists, the BioSAXS beamline allows manual and automatic sample loading/unloading. A Pilatus 1M detector (Dectris) is employed for data collection, characterized by a high dynamic range and a short readout time. The highly automated data processing pipeline SASFLOW was integrated into BL19U2, with help from the BioSAXS group of the European Molecular Biology Laboratory (EMBL, Hamburg), which provides a user-friendly interface for data processing. The BL19U2 beamline was officially opened to users in March 2015. To date, feedback from users has been positive and the number of experimental proposals at BL19U2 is increasing. A description of the new BioSAXS beamline and the setup characteristics is given, together with examples of data obtained.text/htmlThe new NCPSS BL19U2 beamline at the SSRF for small-angle X-ray scattering from biological macromolecules in solutionThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-08-101428research papers1600-5767October 2016med@iucr.org14321600-5767Simultaneous small-angle neutron scattering and Fourier transform infrared spectroscopic measurements on cocrystals of syndiotactic polystyrene with polyethylene glycol dimethyl ethersThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).http://scripts.iucr.org/cgi-bin/paper?jk5009
Syndiotactic polystyrene (sPS) is a crystalline polymer which has a unique property; it is able to form cocrystals with a wide range of chemical compounds, in which the guest molecules are confined in the vacancies of the host sPS crystalline region. Recently, it has been found that even polyethylene glycol oligomers with a molecular weight of more than several hundreds can be introduced into the sPS crystalline region. It is quite important to know how such a long-chain molecule is stored in the host sPS lattice. To tackle this issue, a new simultaneous measurement method combing small-angle neutron scattering and Fourier transform infrared spectroscopy (SANS/FTIR), which has been recently developed by the authors, was applied to an sPS cocrystal with polyethylene glycol dimethyl ether with a molecular weight of 500 (PEGDME500). The temperature-dependent changes of the SANS profile and FTIR spectrum were followed from room temperature up to 413 K for a one-dimensionally oriented SANS/PEGDME500 cocrystal sample. The intensity of the reflections due to the stacking of crystalline lamellae showed a significant temperature dependence. The two-dimensional pattern in the high Q region of SANS also changed depending on temperature. The combined information obtained by SANS and FTIR suggested that PEGDME500 molecules are distributed in both the crystalline and amorphous regions in the low-temperature region close to room temperature, but they are predominantly included in the amorphous region in the high-temperature region. It was also suggested by the two-dimensional SANS profile that PEGDME500 molecules in the crystalline region have an elongated structure along the thickness direction of the crystalline lamellae.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Kaneko, F.Seto, N.Sato, S.Radulescu, A.Schiavone, M.M.Allgaier, J.Ute, K.2016-08-04doi:10.1107/S160057671601178XInternational Union of CrystallographyA new simultaneous measurement method combining small-angle neutron scattering and Fourier-transform infrared spectroscopy was applied to a study on a syndiotactic polystyrene cocrystal with polyethylene glycol dimethyl ether with a molecular weight of 500. It is suggested that the guest molecules in the crystalline region have an elongated structure along the thickness direction of the crystalline lamellae.enCOCRYSTALS; SYNDIOTACTIC POLYSTYRENE; SIMULTANEOUS MEASUREMENT; SMALL-ANGLE NEUTRON SCATTERING; FOURIER TRANSFORM IR SPECTROSCOPYSyndiotactic polystyrene (sPS) is a crystalline polymer which has a unique property; it is able to form cocrystals with a wide range of chemical compounds, in which the guest molecules are confined in the vacancies of the host sPS crystalline region. Recently, it has been found that even polyethylene glycol oligomers with a molecular weight of more than several hundreds can be introduced into the sPS crystalline region. It is quite important to know how such a long-chain molecule is stored in the host sPS lattice. To tackle this issue, a new simultaneous measurement method combing small-angle neutron scattering and Fourier transform infrared spectroscopy (SANS/FTIR), which has been recently developed by the authors, was applied to an sPS cocrystal with polyethylene glycol dimethyl ether with a molecular weight of 500 (PEGDME500). The temperature-dependent changes of the SANS profile and FTIR spectrum were followed from room temperature up to 413 K for a one-dimensionally oriented SANS/PEGDME500 cocrystal sample. The intensity of the reflections due to the stacking of crystalline lamellae showed a significant temperature dependence. The two-dimensional pattern in the high Q region of SANS also changed depending on temperature. The combined information obtained by SANS and FTIR suggested that PEGDME500 molecules are distributed in both the crystalline and amorphous regions in the low-temperature region close to room temperature, but they are predominantly included in the amorphous region in the high-temperature region. It was also suggested by the two-dimensional SANS profile that PEGDME500 molecules in the crystalline region have an elongated structure along the thickness direction of the crystalline lamellae.text/htmlSimultaneous small-angle neutron scattering and Fourier transform infrared spectroscopic measurements on cocrystals of syndiotactic polystyrene with polyethylene glycol dimethyl ethersThis article will form part of a virtual special issue of the journal, presenting some highlights of the 16th International Conference on Small-Angle Scattering (SAS2015).text495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-08-041420research papers1600-5767October 2016med@iucr.org14271600-5767A rapid two-dimensional data collection system for the study of ferroelectric materials under external applied electric fieldshttp://scripts.iucr.org/cgi-bin/paper?kc5040
Synchrotron X-rays on the Swiss Norwegian Beamline and BM28 (XMaS) at the ESRF have been used to record the diffraction response of the PMN–PT relaxor piezoelectric 67% Pb(Mg1/3Nb2/3)O3–33% PbTiO3 as a function of externally applied electric field. A DC field in the range 0–18 kV cm−1 was applied along the [001] pseudo-cubic direction using a specially designed sample cell for in situ single-crystal diffraction experiments. The cell allowed data to be collected on a Pilatus 2M area detector in a large volume of reciprocal space using transmission geometry. The data showed good agreement with a twinned single-phase monoclinic structure model. The results from the area detector were compared with previous Bragg peak mapping using variable electric fields and a single detector where the structural model was ambiguous. The coverage of a significantly larger section of reciprocal space facilitated by the area detector allowed precise phase analysis.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Vergentev, T.Bronwald, I.Chernyshov, D.Gorfman, S.Ryding, S.H.M.Thompson, P.Cernik, R.J.2016-08-16doi:10.1107/S1600576716011341International Union of CrystallographyThe diffraction response of the PMN–PT relaxor piezoelectric 67% Pb(Mg1/3Nb2/3)O3–33% PbTiO3 has been recorded as a function of externally applied electric field. The DC field was applied using a specially designed sample cell for in situ single-crystal diffraction experiments. The coverage of a significantly large section of reciprocal space allowed precise phase analysis.enFERROELECTRICITY; PIEZOELECTRICITY; DIFFUSE SCATTERING; IN SITU TWO-DIMENSIONAL X-RAY SINGLE-CRYSTAL DIFFRACTION; AREA DETECTORS; SYNCHROTRON X-RAYS; PMN-PT; PHASE TRANSITIONSSynchrotron X-rays on the Swiss Norwegian Beamline and BM28 (XMaS) at the ESRF have been used to record the diffraction response of the PMN–PT relaxor piezoelectric 67% Pb(Mg1/3Nb2/3)O3–33% PbTiO3 as a function of externally applied electric field. A DC field in the range 0–18 kV cm−1 was applied along the [001] pseudo-cubic direction using a specially designed sample cell for in situ single-crystal diffraction experiments. The cell allowed data to be collected on a Pilatus 2M area detector in a large volume of reciprocal space using transmission geometry. The data showed good agreement with a twinned single-phase monoclinic structure model. The results from the area detector were compared with previous Bragg peak mapping using variable electric fields and a single detector where the structural model was ambiguous. The coverage of a significantly larger section of reciprocal space facilitated by the area detector allowed precise phase analysis.text/htmlA rapid two-dimensional data collection system for the study of ferroelectric materials under external applied electric fieldstext495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-08-161501research papers1600-5767October 2016med@iucr.org15071600-5767US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS datahttp://scripts.iucr.org/cgi-bin/paper?vg5038
Size-exclusion chromatography coupled with SAXS (small-angle X-ray scattering), often performed using a flow-through capillary, should allow direct collection of monodisperse sample data. However, capillary fouling issues and non-baseline-resolved peaks can hamper its efficacy. The UltraScan solution modeler (US-SOMO) HPLC-SAXS (high-performance liquid chromatography coupled with SAXS) module provides a comprehensive framework to analyze such data, starting with a simple linear baseline correction and symmetrical Gaussian decomposition tools [Brookes, Pérez, Cardinali, Profumo, Vachette & Rocco (2013). J. Appl. Cryst. 46, 1823–1833]. In addition to several new features, substantial improvements to both routines have now been implemented, comprising the evaluation of outcomes by advanced statistical tools. The novel integral baseline-correction procedure is based on the more sound assumption that the effect of capillary fouling on scattering increases monotonically with the intensity scattered by the material within the X-ray beam. Overlapping peaks, often skewed because of sample interaction with the column matrix, can now be accurately decomposed using non-symmetrical modified Gaussian functions. As an example, the case of a polydisperse solution of aldolase is analyzed: from heavily convoluted peaks, individual SAXS profiles of tetramers, octamers and dodecamers are extracted and reliably modeled.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Brookes, E.Vachette, P.Rocco, M.Pérez, J.2016-09-01doi:10.1107/S1600576716011201International Union of CrystallographyThe US-SOMO HPLC-SAXS (high-performance liquid chromatography coupled with small-angle X-ray scattering) module is an advanced tool for the comprehensive analysis of SEC-SAXS (size-exclusion chromatography coupled with SAXS) data. It includes baseline and band-broadening correction routines, and Gaussian decomposition of overlapping skewed peaks into pure components.enPOORLY RESOLVED CHROMATOGRAPHIC PEAKS; ASYMMETRIC MODIFIED GAUSSIAN DECOMPOSITION; MULTI-RESOLUTION MODELING; ALDOLASE SUPRAMOLECULAR COMPLEXES; P-VALUE ANALYSIS; CORMAP ANALYSIS; US-SOMO HPLC-SAXS MODULESize-exclusion chromatography coupled with SAXS (small-angle X-ray scattering), often performed using a flow-through capillary, should allow direct collection of monodisperse sample data. However, capillary fouling issues and non-baseline-resolved peaks can hamper its efficacy. The UltraScan solution modeler (US-SOMO) HPLC-SAXS (high-performance liquid chromatography coupled with SAXS) module provides a comprehensive framework to analyze such data, starting with a simple linear baseline correction and symmetrical Gaussian decomposition tools [Brookes, Pérez, Cardinali, Profumo, Vachette & Rocco (2013). J. Appl. Cryst. 46, 1823–1833]. In addition to several new features, substantial improvements to both routines have now been implemented, comprising the evaluation of outcomes by advanced statistical tools. The novel integral baseline-correction procedure is based on the more sound assumption that the effect of capillary fouling on scattering increases monotonically with the intensity scattered by the material within the X-ray beam. Overlapping peaks, often skewed because of sample interaction with the column matrix, can now be accurately decomposed using non-symmetrical modified Gaussian functions. As an example, the case of a polydisperse solution of aldolase is analyzed: from heavily convoluted peaks, individual SAXS profiles of tetramers, octamers and dodecamers are extracted and reliably modeled.text/htmlUS-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS datatext495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-09-011827computer programs1600-5767October 2016med@iucr.org18411600-5767Guinier peak analysis for visual and automated inspection of small-angle X-ray scattering datahttp://scripts.iucr.org/cgi-bin/paper?vg5047
The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration, Rg, and the forward scattering intensity, I(0). In Guinier peak analysis (GPA), the plot of qI(q) versus q2 transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution function P(r) after and before the P(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Putnam, C.D.2016-08-04doi:10.1107/S1600576716010906International Union of CrystallographyGuinier peak analysis (GPA), derived from the Guinier approximation, transforms the Guinier region of small-angle X-ray scattering data into a characteristic peak that verifies the existence of the Guinier region in the data. Deviation of the Guinier peak position in dimensionless GPA plots can be a useful addition to sample characterization and parameter validation protocols.enSMALL-ANGLE X-RAY SCATTERING; SAMPLE CHARACTERIZATION; GUINIER ANALYSIS; GUINIER PEAK ANALYSIS; ELONGATION RATIOThe Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration, Rg, and the forward scattering intensity, I(0). In Guinier peak analysis (GPA), the plot of qI(q) versus q2 transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution function P(r) after and before the P(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.text/htmlGuinier peak analysis for visual and automated inspection of small-angle X-ray scattering datatext495http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-08-041412research papers1600-5767October 2016med@iucr.org14191600-5767WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulationsThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zd5006
This article describes the WavePropaGator (WPG) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop (SRW) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Samoylova, L.Buzmakov, A.Chubar, O.Sinn, H.2016-07-06doi:10.1107/S160057671600995XInternational Union of CrystallographyThe WavePropaGator (WPG) package is a new interactive cross-platform open-source software framework for modeling of coherent and partially coherent X-ray wavefront propagation. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The paper presents a general description of the package and gives some recent application examples.enWAVEFRONT PROPAGATION; X-RAY FREE-ELECTRON LASERS; XFELS; FOURIER OPTICS; START-TO-END SIMULATIONS; DATA ANALYSIS AND VISUALIZATION; COMPUTER PROGRAMSThis article describes the WavePropaGator (WPG) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop (SRW) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.text/htmlWavePropaGator: interactive framework for X-ray free-electron laser optics design and simulationsThis article will form part of a virtual special issue of the journal on free-electron laser software.text494http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-07-061347computer programs1600-5767August 2016med@iucr.org13551600-5767Rotation of X-ray polarization in the glitches of a silicon crystal monochromatorhttp://scripts.iucr.org/cgi-bin/paper?te5014
EXAFS studies on dilute samples are usually carried out by collecting the fluorescence yield using a large-area multi-element detector. This method is susceptible to the `glitches' produced by all single-crystal monochromators. Glitches are sharp dips or spikes in the diffracted intensity at specific crystal orientations. If incorrectly compensated, they degrade the spectroscopic data. Normalization of the fluorescence signal by the incident flux alone is sometimes insufficient to compensate for the glitches. Measurements performed at the state-of-the-art wiggler beamline I20-scanning at Diamond Light Source have shown that the glitches alter the spatial distribution of the sample's quasi-elastic X-ray scattering. Because glitches result from additional Bragg reflections, multiple-beam dynamical diffraction theory is necessary to understand their effects. Here, the glitches of the Si(111) four-bounce monochromator of I20-scanning just above the Ni K edge are associated with their Bragg reflections. A fitting procedure that treats coherent and Compton scattering is developed and applied to a sample of an extremely dilute (100 micromolal) aqueous solution of Ni(NO3)2. The depolarization of the wiggler X-ray beam out of the electron orbit is modeled. The fits achieve good agreement with the sample's quasi-elastic scattering with just a few parameters. The X-ray polarization is rotated up to ±4.3° within the glitches, as predicted by dynamical diffraction. These results will help users normalize EXAFS data at glitches.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Sutter, J.P.Boada, R.Bowron, D.T.Stepanov, S.A.Díaz-Moreno, S.2016-07-06doi:10.1107/S1600576716009183International Union of CrystallographyRotation of X-ray polarization at the glitches of a monochromator composed of single crystals of silicon is observed. This effect can be explained by a model taking full account of the X-ray source, the effects of multiple-beam dynamical diffraction, and the coherent and Compton scattering from the sample.enX-RAY MONOCHROMATOR GLITCHES; X-RAY POLARIZATION; EXAFSEXAFS studies on dilute samples are usually carried out by collecting the fluorescence yield using a large-area multi-element detector. This method is susceptible to the `glitches' produced by all single-crystal monochromators. Glitches are sharp dips or spikes in the diffracted intensity at specific crystal orientations. If incorrectly compensated, they degrade the spectroscopic data. Normalization of the fluorescence signal by the incident flux alone is sometimes insufficient to compensate for the glitches. Measurements performed at the state-of-the-art wiggler beamline I20-scanning at Diamond Light Source have shown that the glitches alter the spatial distribution of the sample's quasi-elastic X-ray scattering. Because glitches result from additional Bragg reflections, multiple-beam dynamical diffraction theory is necessary to understand their effects. Here, the glitches of the Si(111) four-bounce monochromator of I20-scanning just above the Ni K edge are associated with their Bragg reflections. A fitting procedure that treats coherent and Compton scattering is developed and applied to a sample of an extremely dilute (100 micromolal) aqueous solution of Ni(NO3)2. The depolarization of the wiggler X-ray beam out of the electron orbit is modeled. The fits achieve good agreement with the sample's quasi-elastic scattering with just a few parameters. The X-ray polarization is rotated up to ±4.3° within the glitches, as predicted by dynamical diffraction. These results will help users normalize EXAFS data at glitches.text/htmlRotation of X-ray polarization in the glitches of a silicon crystal monochromatortext494http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-07-061209research papers1600-5767August 2016med@iucr.org12221600-5767Condor: a simulation tool for flash X-ray imagingThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zd5005
Flash X-ray imaging has the potential to determine structures down to molecular resolution without the need for crystallization. The ability to accurately predict the diffraction signal and to identify the optimal experimental configuration within the limits of the instrument is important for successful data collection. This article introduces Condor, an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result. It also aims to support researchers who intend to create or advance reconstruction algorithms by simulating realistic test data. Condor is designed to be easy to use and can be either installed as a Python package or used from its web interface (http://lmb.icm.uu.se/condor). X-ray free-electron lasers have high running costs and beam time at these facilities is precious. Data quality can be substantially improved by using simulations to guide the experimental design and simplify data analysis.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hantke, M.F.Ekeberg, T.Maia, F.R.N.C.2016-07-14doi:10.1107/S1600576716009213International Union of CrystallographyCondor, an open-source simulation tool to predict X-ray scattering amplitudes for flash X-ray imaging experiments, is introduced.enFEMTOSECOND COHERENT DIFFRACTIVE IMAGING; X-RAY FREE-ELECTRON LASERS; SIMULATION; SINGLE-PARTICLE IMAGING; COMPUTER PROGRAMSFlash X-ray imaging has the potential to determine structures down to molecular resolution without the need for crystallization. The ability to accurately predict the diffraction signal and to identify the optimal experimental configuration within the limits of the instrument is important for successful data collection. This article introduces Condor, an open-source simulation tool to predict X-ray far-field scattering amplitudes of isolated particles for customized experimental designs and samples, which the user defines by an atomic or a refractive index model. The software enables researchers to test whether their envisaged imaging experiment is feasible, and to optimize critical parameters for reaching the best possible result. It also aims to support researchers who intend to create or advance reconstruction algorithms by simulating realistic test data. Condor is designed to be easy to use and can be either installed as a Python package or used from its web interface (http://lmb.icm.uu.se/condor). X-ray free-electron lasers have high running costs and beam time at these facilities is precious. Data quality can be substantially improved by using simulations to guide the experimental design and simplify data analysis.text/htmlCondor: a simulation tool for flash X-ray imagingThis article will form part of a virtual special issue of the journal on free-electron laser software.text494http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-07-141356computer programs1600-5767August 2016med@iucr.org13621600-5767CFEL–ASG Software Suite (CASS): usage for free-electron laser experiments with biological focusThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zw5003
CASS [Foucar et al. (2012). Comput. Phys. Commun. 183, 2207–2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Foucar, L.2016-06-23doi:10.1107/S1600576716009201International Union of CrystallographyAn overview of how the well established CFEL–ASG Software Suite (CASS) can be used for serial femtosecond crystallography data is given.enFREE-ELECTRON LASERS; FELS; DATA ANALYSIS; FEMTOSECOND CRYSTALLOGRAPHY; SFX; SINGLE-PARTICLE EXPERIMENTS; PUMP-PROBE TECHNIQUES; FLUORESCENCE; COMPUTER PROGRAMSCASS [Foucar et al. (2012). Comput. Phys. Commun. 183, 2207–2213] is a well established software suite for experiments performed at any sort of light source. It is based on a modular design and can easily be adapted for use at free-electron laser (FEL) experiments that have a biological focus. This article will list all the additional functionality and enhancements of CASS for use with FEL experiments that have been introduced since the first publication. The article will also highlight some advanced experiments with biological aspects that have been performed.text/htmlCFEL–ASG Software Suite (CASS): usage for free-electron laser experiments with biological focusThis article will form part of a virtual special issue of the journal on free-electron laser software.text494http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-06-231336computer programs1600-5767August 2016med@iucr.org13461600-5767Dragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imagingThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zf5002
Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, the Dragonfly software package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ayyer, K.Lan, T.-Y.Elser, V.Loh, N.D.2016-06-20doi:10.1107/S1600576716008165International Union of CrystallographyA description is given of a single-particle X-ray imaging reconstruction and simulation package using the expand–maximize–compress algorithm, named Dragonfly.enSINGLE-PARTICLE IMAGING; X-RAY FREE-ELECTRON LASERS; XFELS; EXPAND-MAXIMIZE-COMPRESS RECONSTRUCTION ALGORITHMSingle-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, the Dragonfly software package is described, based on a parallel implementation of the expand–maximize–compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.text/htmlDragonfly: an implementation of the expand–maximize–compress algorithm for single-particle imagingThis article will form part of a virtual special issue of the journal on free-electron laser software.text494http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-06-201320computer programs1600-5767August 2016med@iucr.org13351600-5767OnDA: online data analysis and feedback for serial X-ray imagingThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zf5001
This article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments: OnDA (online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided. The emphasis here is on simple, modular and scalable code that is based on open-source libraries and protocols. OnDA monitors have already proven to be invaluable tools in several experiments, especially for scoring and monitoring of diffraction data during serial crystallography experiments at both free-electron laser and synchrotron facilities. It is felt that in the future the kind of fast feedback that OnDA monitors provide will help researchers to deal with the expected very high throughput data flow at next-generation facilities such as the European X-ray free-electron laser.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Mariani, V.Morgan, A.Yoon, C.H.Lane, T.J.White, T.A.O'Grady, C.Kuhn, M.Aplin, S.Koglin, J.Barty, A.Chapman, H.N.2016-05-23doi:10.1107/S1600576716007469International Union of CrystallographyThis article describes the software package OnDA: online data analysis and feedback for serial X-ray imaging.enONLINE DATA ANALYSIS; FREE-ELECTRON LASERS; SERIAL FEMTOSECOND CRYSTALLOGRAPHY; COMPUTER PROGRAMSThis article describes a free and open-source data analysis utility designed for fast online feedback during serial X-ray diffraction and scattering experiments: OnDA (online data analysis). Three complete real-time monitors for common types of serial X-ray imaging experiments are presented. These monitors are capable of providing the essential information required for quick decision making in the face of extreme rates of data collection. In addition, a set of modules, functions and algorithms that allow developers to modify the provided monitors or develop new ones are provided. The emphasis here is on simple, modular and scalable code that is based on open-source libraries and protocols. OnDA monitors have already proven to be invaluable tools in several experiments, especially for scoring and monitoring of diffraction data during serial crystallography experiments at both free-electron laser and synchrotron facilities. It is felt that in the future the kind of fast feedback that OnDA monitors provide will help researchers to deal with the expected very high throughput data flow at next-generation facilities such as the European X-ray free-electron laser.text/htmlOnDA: online data analysis and feedback for serial X-ray imagingThis article will form part of a virtual special issue of the journal on free-electron laser software.text3492016-05-23Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1073med@iucr.orgJune 201610801600-5767Measurement and modeling of polarized specular neutron reflectivity in large magnetic fieldshttp://scripts.iucr.org/cgi-bin/paper?ge5021
The presence of a large applied magnetic field removes the degeneracy of the vacuum energy states for spin-up and spin-down neutrons. For polarized neutron reflectometry, this must be included in the reference potential energy of the Schrödinger equation that is used to calculate the expected scattering from a magnetic layered structure. For samples with magnetization that is purely parallel or antiparallel to the applied field which defines the quantization axis, there is no mixing of the spin states (no spin-flip scattering) and so this additional potential is constant throughout the scattering region. When there is non-collinear magnetization in the sample, however, there will be significant scattering from one spin state into the other, and the reference potentials will differ between the incoming and outgoing wavefunctions, changing the angle and intensities of the scattering. The theory of the scattering and recommended experimental practices for this type of measurement are presented, as well as an example measurement.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Maranville, B.B.Kirby, B.J.Grutter, A.J.Kienzle, P.A.Majkrzak, C.F.Liu, Y.Dennis, C.L.2016-06-09doi:10.1107/S1600576716007135International Union of CrystallographyA procedure is described for polarized neutron reflectometry when the Zeeman corrections are significant, which occurs when both the magnetic anisotropy and the applied magnetic field are significant. Calculations and a recommended procedure for an example system are provided.enPOLARIZED NEUTRON REFLECTOMETRY; APPLIED MAGNETIC FIELDS; ZEEMAN CORRECTIONS; NON-COLLINEAR MAGNETIZATIONThe presence of a large applied magnetic field removes the degeneracy of the vacuum energy states for spin-up and spin-down neutrons. For polarized neutron reflectometry, this must be included in the reference potential energy of the Schrödinger equation that is used to calculate the expected scattering from a magnetic layered structure. For samples with magnetization that is purely parallel or antiparallel to the applied field which defines the quantization axis, there is no mixing of the spin states (no spin-flip scattering) and so this additional potential is constant throughout the scattering region. When there is non-collinear magnetization in the sample, however, there will be significant scattering from one spin state into the other, and the reference potentials will differ between the incoming and outgoing wavefunctions, changing the angle and intensities of the scattering. The theory of the scattering and recommended experimental practices for this type of measurement are presented, as well as an example measurement.text/htmlMeasurement and modeling of polarized specular neutron reflectivity in large magnetic fieldstext494http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-06-091121research papers1600-5767August 2016med@iucr.org11291600-5767Modeling truncated pixel values of faint reflections in MicroED imagesThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zw5007
The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hattne, J.Shi, D.Cruz, M.J. de laReyes, F.E.Gonen, T.2016-05-11doi:10.1107/S1600576716007196International Union of CrystallographyA procedure is presented to model the truncated low pixel counts in micro-electron diffraction (MicroED) images. The correction could extend to any conventional macromolecular X-ray crystallography or X-ray free-electron laser measurements.enCRYOEM; MICRO-ELECTRON DIFFRACTION; MICROED; X-RAY FREE-ELECTRON LASERS; XFELSThe weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images.text/htmlModeling truncated pixel values of faint reflections in MicroED imagesThis article will form part of a virtual special issue of the journal on free-electron laser software.text3492016-05-11Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1029med@iucr.orgJune 201610341600-5767On the release of cppxfel for processing X-ray free-electron laser imagesThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zw5002
As serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ginn, H.M.Evans, G.Sauter, N.K.Stuart, D.I.2016-05-11doi:10.1107/S1600576716006981International Union of CrystallographyHere cppxfel, a software package for integration and post-refinement of serial femtosecond crystallography data, is released.enX-RAY FREE-ELECTRON LASERS; XFELS; SERIAL FEMTOSECOND CRYSTALLOGRAPHY; DATA ANALYSIS; COMPUTER PROGRAMSAs serial femtosecond crystallography expands towards a variety of delivery methods, including chip-based methods, and smaller collected data sets, the requirement to optimize the data analysis to produce maximum structure quality is becoming increasingly pressing. Here cppxfel, a software package primarily written in C++, which showcases several data analysis techniques, is released. This software package presently indexes images using DIALS (diffraction integration for advanced light sources) and performs an initial orientation matrix refinement, followed by post-refinement of individual images against a reference data set. Cppxfel is released with the hope that the unique and useful elements of this package can be repurposed for existing software packages. However, as released, it produces high-quality crystal structures and is therefore likely to be also useful to experienced users of X-ray free-electron laser (XFEL) software who wish to maximize the information extracted from a limited number of XFEL images.text/htmlOn the release of cppxfel for processing X-ray free-electron laser imagesThis article will form part of a virtual special issue of the journal on free-electron laser software.text3492016-05-11Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1065med@iucr.orgJune 201610721600-5767Investigation of dissimilar metal welds by energy-resolved neutron imaginghttp://scripts.iucr.org/cgi-bin/paper?ks5507
A nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participating alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al–steel weld is clearly resolved and could be used to optimize the welding process. A highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Tremsin, A.S.Ganguly, S.Meco, S.M.Pardal, G.R.Shinohara, T.Feller, W.B.2016-06-09doi:10.1107/S1600576716006725International Union of CrystallographyEnergy-resolved neutron imaging is used for a nondestructive study of bulk internal microstructure, elemental composition and distribution of voids in dissimilar metal-alloy welds of ∼10 mm thickness. All these characteristics are measured simultaneously in one experiment with a few hundred micrometre spatial resolution.enNONDESTRUCTIVE TESTING; LASER WELDING; DISSIMILAR JOINING; MICROSTRUCTURE; NEUTRON IMAGINGA nondestructive study of the internal structure and compositional gradient of dissimilar metal-alloy welds through energy-resolved neutron imaging is described in this paper. The ability of neutrons to penetrate thick metal objects (up to several cm) provides a unique possibility to examine samples which are opaque to other conventional techniques. The presence of Bragg edges in the measured neutron transmission spectra can be used to characterize the internal residual strain within the samples and some microstructural features, e.g. texture within the grains, while neutron resonance absorption provides the possibility to map the degree of uniformity in mixing of the participating alloys and intermetallic formation within the welds. In addition, voids and other defects can be revealed by the variation of neutron attenuation across the samples. This paper demonstrates the potential of neutron energy-resolved imaging to measure all these characteristics simultaneously in a single experiment with sub-mm spatial resolution. Two dissimilar alloy welds are used in this study: Al autogenously laser welded to steel, and Ti gas metal arc welded (GMAW) to stainless steel using Cu as a filler alloy. The cold metal transfer variant of the GMAW process was used in joining the Ti to the stainless steel in order to minimize the heat input. The distributions of the lattice parameter and texture variation in these welds as well as the presence of voids and defects in the melt region are mapped across the welds. The depth of the thermal front in the Al–steel weld is clearly resolved and could be used to optimize the welding process. A highly textured structure is revealed in the Ti to stainless steel joint where copper was used as a filler wire. The limited diffusion of Ti into the weld region is also verified by the resonance absorption.text/htmlInvestigation of dissimilar metal welds by energy-resolved neutron imagingtext494http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2016-06-091130research papers1600-5767August 2016med@iucr.org11401600-5767IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction imagesThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?gm5045
Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Lyubimov, A.Y.Uervirojnangkoorn, M.Zeldin, O.B.Brewster, A.S.Murray, T.D.Sauter, N.K.Berger, J.M.Weis, W.I.Brunger, A.T.2016-05-11doi:10.1107/S1600576716006683International Union of CrystallographyAn integration optimization, triage and analysis tool (IOTA) is presented, which uses a grid-search approach to maximize the success of indexing and integrating serial X-ray free-electron laser diffraction images. IOTA also includes several useful tools for on-site diffraction data processing.enDIFFRACTION DATA PROCESSING; X-RAY FREE-ELECTRON LASERS; XFELS; SERIAL FEMTOSECOND CRYSTALLOGRAPHY; INDEXING AND INTEGRATION; COMPUTER PROGRAMSSerial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.text/htmlIOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction imagesThis article will form part of a virtual special issue of the journal on free-electron laser software.text3492016-05-11Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1057med@iucr.orgJune 201610641600-5767Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scatteringhttp://scripts.iucr.org/cgi-bin/paper?fs5133
Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of D1/2 = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Roedig, P.Duman, R.Sanchez-Weatherby, J.Vartiainen, I.Burkhardt, A.Warmer, M.David, C.Wagner, A.Meents, A.2016-05-23doi:10.1107/S1600576716006348International Union of CrystallographyA micro-patterned sample holder of single-crystalline silicon, loaded with multiple protein crystals which are exposed to a humidified gas stream, allows high-quality room-temperature data collection.enCRYSTALLOGRAPHY ON A CHIP; SYNCHROTRON SERIAL CRYSTALLOGRAPHY; ROOM-TEMPERATURE CRYSTALLOGRAPHY; X-RAY RADIATION DAMAGERecent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of D1/2 = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.text/htmlRoom-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scatteringtext3492016-05-23Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers968med@iucr.orgJune 20169751600-5767Fast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystalshttp://scripts.iucr.org/cgi-bin/paper?ap5003
A fast continuous grid scan protocol has been incorporated into the Swiss Light Source (SLS) data acquisition and analysis software suite on the macromolecular crystallography (MX) beamlines. Its combination with fast readout single-photon counting hybrid pixel array detectors (PILATUS and EIGER) allows for diffraction-based identification of crystal diffraction hotspots and the location and centering of membrane protein microcrystals in the lipid cubic phase (LCP) in in meso in situ serial crystallography plates and silicon nitride supports. Diffraction-based continuous grid scans with both still and oscillation images are supported. Examples that include a grid scan of a large (50 nl) LCP bolus and analysis of the resulting diffraction images are presented. Scanning transmission X-ray microscopy (STXM) complements and benefits from fast grid scanning. STXM has been demonstrated at the SLS beamline X06SA for near-zero-dose detection of protein crystals mounted on different types of sample supports at room and cryogenic temperatures. Flash-cooled crystals in nylon loops were successfully identified in differential and integrated phase images. Crystals of just 10 µm thickness were visible in integrated phase images using data collected with the EIGER detector. STXM offers a truly low-dose method for locating crystals on solid supports prior to diffraction data collection at both synchrotron microfocusing and free-electron laser X-ray facilities.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Wojdyla, J.A.Panepucci, E.Martiel, I.Ebner, S.Huang, C.-Y.Caffrey, M.Bunk, O.Wang, M.2016-05-16doi:10.1107/S1600576716006233International Union of CrystallographyThis article reports the incorporation of a fast continuous grid scan with both still and oscillation images into the Swiss Light Source macromolecular crystallography beamlines and its application in visualization of protein crystals with scanning transmission X-ray microscopy.enMACROMOLECULAR CRYSTALLOGRAPHY; FAST GRID SCANS; OSCILLATION IMAGES; SCANNING TRANSMISSION X-RAY MICROSCOPY; VISUALIZATION OF PROTEIN CRYSTALSA fast continuous grid scan protocol has been incorporated into the Swiss Light Source (SLS) data acquisition and analysis software suite on the macromolecular crystallography (MX) beamlines. Its combination with fast readout single-photon counting hybrid pixel array detectors (PILATUS and EIGER) allows for diffraction-based identification of crystal diffraction hotspots and the location and centering of membrane protein microcrystals in the lipid cubic phase (LCP) in in meso in situ serial crystallography plates and silicon nitride supports. Diffraction-based continuous grid scans with both still and oscillation images are supported. Examples that include a grid scan of a large (50 nl) LCP bolus and analysis of the resulting diffraction images are presented. Scanning transmission X-ray microscopy (STXM) complements and benefits from fast grid scanning. STXM has been demonstrated at the SLS beamline X06SA for near-zero-dose detection of protein crystals mounted on different types of sample supports at room and cryogenic temperatures. Flash-cooled crystals in nylon loops were successfully identified in differential and integrated phase images. Crystals of just 10 µm thickness were visible in integrated phase images using data collected with the EIGER detector. STXM offers a truly low-dose method for locating crystals on solid supports prior to diffraction data collection at both synchrotron microfocusing and free-electron laser X-ray facilities.text/htmlFast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystalstext3492016-05-16Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers944med@iucr.orgJune 20169521600-5767Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real timeThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zd5007
Advances in X-ray detectors and increases in the brightness of X-ray sources combined with more efficient sample delivery techniques have brought about tremendous increases in the speed of data collection in diffraction experiments. Using X-ray free-electron lasers such as the Linac Coherent Light Source (LCLS), more than 100 diffraction patterns can be collected in a second. These high data rates are invaluable for flash X-ray imaging (FXI), where aerosolized samples are exposed to the X-ray beam and the resulting diffraction patterns are used to reconstruct a three-dimensional image of the sample. Such experiments require immediate feedback on the quality of the data collected to adjust or validate experimental parameters, such as aerosol injector settings, beamline geometry or sample composition. The scarcity of available beamtime at the laser facilities makes any delay extremely costly. This paper presents Hummingbird, an open-source scalable Python-based software tool for real-time analysis of diffraction data with the purpose of giving users immediate feedback during their experiments. Hummingbird provides a fast, flexible and easy-to-use framework. It has already proven to be of great value in numerous FXI experiments at the LCLS.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Daurer, B.J.Hantke, M.F.Nettelblad, C.Maia, F.R.N.C.2016-04-18doi:10.1107/S1600576716005926International Union of CrystallographyHummingbird is an open-source scalable Python-based software tool for real-time analysis of diffraction data with the purpose of giving users immediate feedback during their experiments.enX-RAY FREE-ELECTRON LASERS; XFELS; FLASH X-RAY IMAGING; REAL-TIME DATA ANALYSIS; COMPUTER PROGRAMSAdvances in X-ray detectors and increases in the brightness of X-ray sources combined with more efficient sample delivery techniques have brought about tremendous increases in the speed of data collection in diffraction experiments. Using X-ray free-electron lasers such as the Linac Coherent Light Source (LCLS), more than 100 diffraction patterns can be collected in a second. These high data rates are invaluable for flash X-ray imaging (FXI), where aerosolized samples are exposed to the X-ray beam and the resulting diffraction patterns are used to reconstruct a three-dimensional image of the sample. Such experiments require immediate feedback on the quality of the data collected to adjust or validate experimental parameters, such as aerosol injector settings, beamline geometry or sample composition. The scarcity of available beamtime at the laser facilities makes any delay extremely costly. This paper presents Hummingbird, an open-source scalable Python-based software tool for real-time analysis of diffraction data with the purpose of giving users immediate feedback during their experiments. Hummingbird provides a fast, flexible and easy-to-use framework. It has already proven to be of great value in numerous FXI experiments at the LCLS.text/htmlHummingbird: monitoring and analyzing flash X-ray imaging experiments in real timeThis article will form part of a virtual special issue of the journal on free-electron laser software.text3492016-04-18Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1042med@iucr.orgJune 201610471600-5767Rapid automated superposition of shapes and macromolecular models using spherical harmonicshttp://scripts.iucr.org/cgi-bin/paper?ap5002
A rapid algorithm to superimpose macromolecular models in Fourier space is proposed and implemented (SUPALM). The method uses a normalized integrated cross-term of the scattering amplitudes as a proximity measure between two three-dimensional objects. The reciprocal-space algorithm allows for direct matching of heterogeneous objects including high- and low-resolution models represented by atomic coordinates, beads or dummy residue chains as well as electron microscopy density maps and inhomogeneous multi-phase models (e.g. of protein–nucleic acid complexes). Using spherical harmonics for the computation of the amplitudes, the method is up to an order of magnitude faster than the real-space algorithm implemented in SUPCOMB by Kozin & Svergun [J. Appl. Cryst. (2001), 34, 33–41]. The utility of the new method is demonstrated in a number of test cases and compared with the results of SUPCOMB. The spherical harmonics algorithm is best suited for low-resolution shape models, e.g. those provided by solution scattering experiments, but also facilitates a rapid cross-validation against structural models obtained by other methods.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Konarev, P.V.Petoukhov, M.V.Svergun, D.I.2016-05-16doi:10.1107/S1600576716005793International Union of CrystallographyA method utilizing a spherical harmonics representation of the scattering amplitudes for a rapid superposition of three-dimensional models is developed.enSMALL-ANGLE SCATTERING; PROTEIN STRUCTURE; MODEL SUPERPOSITION; SCATTERING AMPLITUDES; SUPALMA rapid algorithm to superimpose macromolecular models in Fourier space is proposed and implemented (SUPALM). The method uses a normalized integrated cross-term of the scattering amplitudes as a proximity measure between two three-dimensional objects. The reciprocal-space algorithm allows for direct matching of heterogeneous objects including high- and low-resolution models represented by atomic coordinates, beads or dummy residue chains as well as electron microscopy density maps and inhomogeneous multi-phase models (e.g. of protein–nucleic acid complexes). Using spherical harmonics for the computation of the amplitudes, the method is up to an order of magnitude faster than the real-space algorithm implemented in SUPCOMB by Kozin & Svergun [J. Appl. Cryst. (2001), 34, 33–41]. The utility of the new method is demonstrated in a number of test cases and compared with the results of SUPCOMB. The spherical harmonics algorithm is best suited for low-resolution shape models, e.g. those provided by solution scattering experiments, but also facilitates a rapid cross-validation against structural models obtained by other methods.text/htmlRapid automated superposition of shapes and macromolecular models using spherical harmonicstext3492016-05-16Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers953med@iucr.orgJune 20169601600-5767Data processing pipeline for serial femtosecond crystallography at SACLAThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zw5001
A data processing pipeline for serial femtosecond crystallography at SACLA was developed, based on Cheetah [Barty et al. (2014). J. Appl. Cryst. 47, 1118–1131] and CrystFEL [White et al. (2016). J. Appl. Cryst. 49, 680–689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runs CrystFEL for indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Nakane, T.Joti, Y.Tono, K.Yabashi, M.Nango, E.Iwata, S.Ishitani, R.Nureki, O.2016-04-18doi:10.1107/S1600576716005720International Union of CrystallographyA data processing pipeline for SACLA was developed, based on Cheetah and CrystFEL. Real-time analysis and rapid structure solution were enabled.enSERIAL FEMTOSECOND CRYSTALLOGRAPHY; REAL-TIME PROCESSING; SPOT FINDING; PARALLELIZATION; SACLAA data processing pipeline for serial femtosecond crystallography at SACLA was developed, based on Cheetah [Barty et al. (2014). J. Appl. Cryst. 47, 1118–1131] and CrystFEL [White et al. (2016). J. Appl. Cryst. 49, 680–689]. The original programs were adapted for data acquisition through the SACLA API, thread and inter-node parallelization, and efficient image handling. The pipeline consists of two stages: The first, online stage can analyse all images in real time, with a latency of less than a few seconds, to provide feedback on hit rate and detector saturation. The second, offline stage converts hit images into HDF5 files and runs CrystFEL for indexing and integration. The size of the filtered compressed output is comparable to that of a synchrotron data set. The pipeline enables real-time feedback and rapid structure solution during beamtime.text/htmlData processing pipeline for serial femtosecond crystallography at SACLAThis article will form part of a virtual special issue of the journal on free-electron laser software.text3492016-04-18Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1035med@iucr.orgJune 201610411600-5767Neutron and hard X-ray diffraction studies of the isothermal transformation kinetics in the research reactor fuel candidate U–8 wt%Mohttp://scripts.iucr.org/cgi-bin/paper?ks5499
Exposing uranium–molybdenum alloys (UMo) retained in the γ phase to elevated temperatures leads to transformation reactions during which the γ-UMo phase decomposes into the thermal equilibrium phases, i.e. U2Mo and α-U. Since α-U is not suitable for a nuclear fuel exposed to high burn-up, it is necessary to retain the γ-UMo phase during the production process of the fuel elements for modern high-performance research reactors. The present work deals with the isothermal transformation kinetics in U–8 wt%Mo alloys for temperatures between 673 and 798 K and annealing durations of up to 48 h. Annealed samples were examined at room temperature using either X-ray or neutron diffraction to determine the phase composition after thermal treatment, and in situ annealing studies disclosed the onset of phase decomposition. While for temperatures of 698 and 673 K the start of decomposition is delayed, for higher temperatures the first signs of transformation are already observable within 3 h of annealing. The typical C-shaped curves in a time–temperature–transformation (TTT) diagram for both the start and the end of phase decomposition could be determined in the observed temperature regime. Therefore, a revised TTT diagram for U–8 wt%Mo between 673 and 798 K and annealing durations of up to 48 h is proposed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Säubert, S.Jungwirth, R.Zweifel, T.Hofmann, M.Hoelzel, M.Petry, W.2016-05-16doi:10.1107/S1600576716005744International Union of CrystallographyThe nuclear fuel candidate U–8 wt%Mo has been investigated by means of neutron and hard X-ray diffraction, revealing the isothermal transformation kinetics of the high-temperature γ-UMo phase into its thermal equilibrium microstructures.enURANIUM; NUCLEAR FUELS; URANIUM-MOLYBDENUM ALLOYS; ISOTHERMAL TRANSFORMATION KINETICS; X-RAY DIFFRACTION; NEUTRON DIFFRACTIONExposing uranium–molybdenum alloys (UMo) retained in the γ phase to elevated temperatures leads to transformation reactions during which the γ-UMo phase decomposes into the thermal equilibrium phases, i.e. U2Mo and α-U. Since α-U is not suitable for a nuclear fuel exposed to high burn-up, it is necessary to retain the γ-UMo phase during the production process of the fuel elements for modern high-performance research reactors. The present work deals with the isothermal transformation kinetics in U–8 wt%Mo alloys for temperatures between 673 and 798 K and annealing durations of up to 48 h. Annealed samples were examined at room temperature using either X-ray or neutron diffraction to determine the phase composition after thermal treatment, and in situ annealing studies disclosed the onset of phase decomposition. While for temperatures of 698 and 673 K the start of decomposition is delayed, for higher temperatures the first signs of transformation are already observable within 3 h of annealing. The typical C-shaped curves in a time–temperature–transformation (TTT) diagram for both the start and the end of phase decomposition could be determined in the observed temperature regime. Therefore, a revised TTT diagram for U–8 wt%Mo between 673 and 798 K and annealing durations of up to 48 h is proposed.text/htmlNeutron and hard X-ray diffraction studies of the isothermal transformation kinetics in the research reactor fuel candidate U–8 wt%Motext3492016-05-16Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers923med@iucr.orgJune 20169331600-5767Ultra-small-angle neutron scattering with azimuthal asymmetryhttp://scripts.iucr.org/cgi-bin/paper?ks5503
Small-angle neutron scattering (SANS) measurements from thin sections of rock samples such as shales demand as great a scattering vector range as possible because the pores cover a wide range of sizes. The limitation of the scattering vector range for pinhole SANS requires slit-smeared ultra-SANS (USANS) measurements that need to be converted to pinhole geometry. The desmearing algorithm is only successful for azimuthally symmetric data. Scattering from samples cut parallel to the plane of bedding is symmetric, exhibiting circular contours on a two-dimensional detector. Samples cut perpendicular to the bedding show elliptically dependent contours with the long axis corresponding to the normal to the bedding plane. A method is given for converting such asymmetric data collected on a double-crystal diffractometer for concatenation with the usual pinhole-geometry SANS data. The aspect ratio from the SANS data is used to modify the slit-smeared USANS data to produce quasi-symmetric contours. Rotation of the sample about the incident beam may result in symmetric data but cannot extract the same information as obtained from pinhole geometry.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Gu, X.Mildner, D.F.R.2016-05-16doi:10.1107/S1600576716005586International Union of CrystallographyA method is given for converting slit-smeared azimuthally asymmetric data collected on a double-crystal diffractometer for concatenation with the usual pinhole-geometry small-angle neuton scattering data.enAZIMUTHAL ASYMMETRIC SCATTERING; DOUBLE-CRYSTAL DIFFRACTOMETERS; ELLIPTIC SCATTERING CONTOURS; SLIT-HEIGHT SMEARED SCATTERING; SMALL-ANGLE NEUTRON SCATTERINGSmall-angle neutron scattering (SANS) measurements from thin sections of rock samples such as shales demand as great a scattering vector range as possible because the pores cover a wide range of sizes. The limitation of the scattering vector range for pinhole SANS requires slit-smeared ultra-SANS (USANS) measurements that need to be converted to pinhole geometry. The desmearing algorithm is only successful for azimuthally symmetric data. Scattering from samples cut parallel to the plane of bedding is symmetric, exhibiting circular contours on a two-dimensional detector. Samples cut perpendicular to the bedding show elliptically dependent contours with the long axis corresponding to the normal to the bedding plane. A method is given for converting such asymmetric data collected on a double-crystal diffractometer for concatenation with the usual pinhole-geometry SANS data. The aspect ratio from the SANS data is used to modify the slit-smeared USANS data to produce quasi-symmetric contours. Rotation of the sample about the incident beam may result in symmetric data but cannot extract the same information as obtained from pinhole geometry.text/htmlUltra-small-angle neutron scattering with azimuthal asymmetrytext3492016-05-16Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers934med@iucr.orgJune 20169431600-5767Identification of rogue datasets in serial crystallographyThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zw5005
Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC1/2 [Karplus & Diederichs (2012). Science, 336, 1030–1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC1/2 that avoids the random assignment, and instead of using an overall CC1/2, an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Assmann, G.Brehm, W.Diederichs, K.2016-04-18doi:10.1107/S1600576716005471International Union of CrystallographyIn serial crystallography, CC1/2 may be used as an optimization target, and outlier datasets can be identified on the basis of their influence on the average CC1/2 of the merged data. This leads to the ΔCC1/2 method presented here.enSERIAL CRYSTALLOGRAPHY; OUTLIER IDENTIFICATION; CC1/2; PRECISION; MODEL BIAS; ISOMORPHISM; NON-ISOMORPHISMAdvances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC1/2 [Karplus & Diederichs (2012). Science, 336, 1030–1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC1/2 that avoids the random assignment, and instead of using an overall CC1/2, an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested.text/htmlIdentification of rogue datasets in serial crystallographyThis article will form part of a virtual special issue of the journal on free-electron laser software.text3492016-04-18Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1021med@iucr.orgJune 201610281600-5767Recent developments in CrystFELThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zd5001
CrystFEL is a suite of programs for processing data from `serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. The CrystFEL software suite has been under development since 2009, just before the first hard FEL experiments were performed, and has been significantly updated and improved since then. This article describes the most important improvements which have been made to CrystFEL since the first release version. These changes include the addition of new programs to the suite, the ability to resolve `indexing ambiguities' and several ways to improve the quality of the integrated data by more accurately modelling the underlying diffraction physics.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767White, T.A.Mariani, V.Brehm, W.Yefanov, O.Barty, A.Beyerlein, K.R.Chervinskii, F.Galli, L.Gati, C.Nakane, T.Tolstikova, A.Yamashita, K.Yoon, C.H.Diederichs, K.Chapman, H.N.2016-03-29doi:10.1107/S1600576716004751International Union of CrystallographyDevelopments in the CrystFEL software suite, for processing diffraction data from `serial crystallography' experiments, are described.enDATA PROCESSING; SERIAL CRYSTALLOGRAPHY; X-RAY FREE-ELECTRON LASERS; XFELS; COMPUTER PROGRAMSCrystFEL is a suite of programs for processing data from `serial crystallography' experiments, which are usually performed using X-ray free-electron lasers (FELs) but also increasingly with other X-ray sources. The CrystFEL software suite has been under development since 2009, just before the first hard FEL experiments were performed, and has been significantly updated and improved since then. This article describes the most important improvements which have been made to CrystFEL since the first release version. These changes include the addition of new programs to the suite, the ability to resolve `indexing ambiguities' and several ways to improve the quality of the integrated data by more accurately modelling the underlying diffraction physics.text/htmlRecent developments in CrystFELThis article will form part of a virtual special issue of the journal on free-electron laser software.text2492016-03-29Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs680med@iucr.orgApril 20166891600-5767A crystallization apparatus for temperature-controlled flow-cell dialysis with real-time visualizationhttp://scripts.iucr.org/cgi-bin/paper?ei5002
Many instrumentation developments in crystallization have concentrated on massive parallelization assays and reduction of sample volume per experiment to find initial crystallization conditions. Yet improving the size and diffraction quality of the crystals for diffraction studies often requires decoupling of crystal nucleation and growth. This in turn requires the control of variables such as precipitant and protein concentration, equilibration rate, and temperature, which are all difficult parameters to control in the existing setups. The success of the temperature-controlled batch method, originally developed to grow very large crystals for neutron crystallography, demonstrated that the rational optimization of crystal growth has potential in structural biology. A temperature-controlled dialysis button has been developed for our previous device, and a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant concentration phase diagrams has been constructed. The presented approach differs from the current paradigm, since it involves serial instead of parallel experiments, exploring multiple crystallization conditions with the same protein sample. The sample is not consumed in the experiment and the conditions can be changed in a reversible fashion, using dialysis with a flowing precipitant reservoir as well as precise temperature control. The control software allows visualization of the crystals, as well as control of the temperature and composition of the crystallization solution. The rational crystallization optimization strategies presented here allow tailoring of crystal size, morphology and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Junius, N.Oksanen, E.Terrien, M.Berzin, C.Ferrer, J.-L.Budayova-Spano, M.2016-04-22doi:10.1107/S1600576716004635International Union of CrystallographyAn apparatus for the optimization of crystal growth using precise temperature control and dialysis combined with real-time visualization has been developed.enOPTIMIZATION OF CRYSTAL GROWTH; PHASE DIAGRAMS; DIALYSIS; TEMPERATURE CONTROL; MACROMOLECULAR CRYSTALLOGRAPHYMany instrumentation developments in crystallization have concentrated on massive parallelization assays and reduction of sample volume per experiment to find initial crystallization conditions. Yet improving the size and diffraction quality of the crystals for diffraction studies often requires decoupling of crystal nucleation and growth. This in turn requires the control of variables such as precipitant and protein concentration, equilibration rate, and temperature, which are all difficult parameters to control in the existing setups. The success of the temperature-controlled batch method, originally developed to grow very large crystals for neutron crystallography, demonstrated that the rational optimization of crystal growth has potential in structural biology. A temperature-controlled dialysis button has been developed for our previous device, and a prototype of an integrated apparatus for the rational optimization of crystal growth by mapping and manipulating temperature–precipitant concentration phase diagrams has been constructed. The presented approach differs from the current paradigm, since it involves serial instead of parallel experiments, exploring multiple crystallization conditions with the same protein sample. The sample is not consumed in the experiment and the conditions can be changed in a reversible fashion, using dialysis with a flowing precipitant reservoir as well as precise temperature control. The control software allows visualization of the crystals, as well as control of the temperature and composition of the crystallization solution. The rational crystallization optimization strategies presented here allow tailoring of crystal size, morphology and diffraction quality, significantly reducing the time, effort and amount of expensive protein material required for structure determination.text/htmlA crystallization apparatus for temperature-controlled flow-cell dialysis with real-time visualizationtext3492016-04-22Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers806med@iucr.orgJune 20168131600-5767DCC: a Swiss army knife for structure factor analysis and validationhttp://scripts.iucr.org/cgi-bin/paper?ap5001
Since 2008, X-ray structure depositions to the Protein Data Bank archive (PDB) have required submission of experimental data in the form of structure factor files. RCSB PDB has developed the program DCC to allow worldwide PDB (wwPDB; http://wwpdb.org) biocurators, using a single command-line program, to invoke a number of third-party software packages to compare the model file with the experimental data. DCC functionality includes structure factor validation, electron-density map generation and slicing, local electron-density analysis, and residual B factor analysis. DCC outputs a summary containing various crystallographic statistics in PDBx/mmCIF format for use in automatic data processing and archiving pipelines.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Yang, H.Peisach, E.Westbrook, J.D.Young, J.Berman, H.M.Burley, S.K.2016-04-18doi:10.1107/S1600576716004428International Union of CrystallographyDCC is a wrapper for third-party software packages to aid in structure factor analysis and validation. As the results are recorded in PDBx/mmCIF format, the output from DCC can be used in automatic data pipelines.enPROTEIN DATA BANK; STRUCTURE FACTOR VALIDATION; UTILITY PROGRAMS; DCCSince 2008, X-ray structure depositions to the Protein Data Bank archive (PDB) have required submission of experimental data in the form of structure factor files. RCSB PDB has developed the program DCC to allow worldwide PDB (wwPDB; http://wwpdb.org) biocurators, using a single command-line program, to invoke a number of third-party software packages to compare the model file with the experimental data. DCC functionality includes structure factor validation, electron-density map generation and slicing, local electron-density analysis, and residual B factor analysis. DCC outputs a summary containing various crystallographic statistics in PDBx/mmCIF format for use in automatic data processing and archiving pipelines.text/htmlDCC: a Swiss army knife for structure factor analysis and validationtext3492016-04-18Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1081med@iucr.orgJune 201610841600-5767In situ diagnostics of the crystal-growth process through neutron imaging: application to scintillatorshttp://scripts.iucr.org/cgi-bin/paper?ks5504
Neutrons are known to be unique probes in situations where other types of radiation fail to penetrate samples and their surrounding structures. In this paper it is demonstrated how thermal and cold neutron radiography can provide time-resolved imaging of materials while they are being processed (e.g. while growing single crystals). The processing equipment, in this case furnaces, and the scintillator materials are opaque to conventional X-ray interrogation techniques. The distribution of the europium activator within a BaBrCl:Eu scintillator (0.1 and 0.5% nominal doping concentrations per mole) is studied in situ during the melting and solidification processes with a temporal resolution of 5–7 s. The strong tendency of the Eu dopant to segregate during the solidification process is observed in repeated cycles, with Eu forming clusters on multiple length scales (only for clusters larger than ∼50 µm, as limited by the resolution of the present experiments). It is also demonstrated that the dopant concentration can be quantified even for very low concentration levels (∼0.1%) in 10 mm thick samples. The interface between the solid and liquid phases can also be imaged, provided there is a sufficient change in concentration of one of the elements with a sufficient neutron attenuation cross section. Tomographic imaging of the BaBrCl:0.1%Eu sample reveals a strong correlation between crystal fractures and Eu-deficient clusters. The results of these experiments demonstrate the unique capabilities of neutron imaging for in situ diagnostics and the optimization of crystal-growth procedures.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Tremsin, A.S.Makowska, M.G.Perrodin, D.Shalapska, T.Khodyuk, I.V.Trtik, P.Boillat, P.Vogel, S.C.Losko, A.S.Strobl, M.Kuhn, L.T.Bizarri, G.A.Bourret-Courchesne, E.D.2016-04-12doi:10.1107/S1600576716004350International Union of CrystallographyThe unique possibilities enabled by neutron imaging for in situ remote diagnostics of microstructural characteristics during crystal growth are demonstrated, even when the materials and surrounding structures are opaque to other more conventional interrogation techniques. Neutron radiography is implemented to image remotely the uniformity of elemental distribution (e.g. dopant concentration) during crystal growth, the location of the liquid/solid interface and the presence of macroscopic crystal defects (e.g. cracks), all with a temporal resolution of 5–7 s.enNEUTRON IMAGING; NON-DESTRUCTIVE TESTING; CRYSTAL GROWTH; SCINTILLATORS; IN SITU DIAGNOSTICSNeutrons are known to be unique probes in situations where other types of radiation fail to penetrate samples and their surrounding structures. In this paper it is demonstrated how thermal and cold neutron radiography can provide time-resolved imaging of materials while they are being processed (e.g. while growing single crystals). The processing equipment, in this case furnaces, and the scintillator materials are opaque to conventional X-ray interrogation techniques. The distribution of the europium activator within a BaBrCl:Eu scintillator (0.1 and 0.5% nominal doping concentrations per mole) is studied in situ during the melting and solidification processes with a temporal resolution of 5–7 s. The strong tendency of the Eu dopant to segregate during the solidification process is observed in repeated cycles, with Eu forming clusters on multiple length scales (only for clusters larger than ∼50 µm, as limited by the resolution of the present experiments). It is also demonstrated that the dopant concentration can be quantified even for very low concentration levels (∼0.1%) in 10 mm thick samples. The interface between the solid and liquid phases can also be imaged, provided there is a sufficient change in concentration of one of the elements with a sufficient neutron attenuation cross section. Tomographic imaging of the BaBrCl:0.1%Eu sample reveals a strong correlation between crystal fractures and Eu-deficient clusters. The results of these experiments demonstrate the unique capabilities of neutron imaging for in situ diagnostics and the optimization of crystal-growth procedures.text/htmlIn situ diagnostics of the crystal-growth process through neutron imaging: application to scintillatorstext3492016-04-12Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers743med@iucr.orgJune 20167551600-5767Facilitating model reconstruction for single-particle scattering using small-angle X-ray scattering methodsThis article will form part of a virtual special issue of the journal on free-electron laser software.http://scripts.iucr.org/cgi-bin/paper?zd5002
X-ray free-electron lasers generate intense femtosecond X-ray pulses, so that high-resolution structure determination becomes feasible from noncrystalline samples, such as single particles or single molecules. At the moment, the orientation of sample particles cannot be precisely controlled, and consequently the unknown orientation needs to be recovered using computational algorithms. This delays the model reconstruction until all the scattering patterns have been re-oriented, which often entails a long elapse of time and until the completion of the experiment. The scattering patterns from single particles or multiple particles can be summed to form a virtual powder diffraction pattern, and the low-resolution region, corresponding to the small-angle X-ray scattering (SAXS) regime, can be analysed using existing SAXS methods. This work presents a pipeline that converts single-particle data sets into SAXS data, from which real-time model reconstruction is achieved using the model retrieval approach implemented in the software package SASTBX [Liu, Hexemer & Zwart (2012). J. Appl. Cryst. 45, 587–593]. To illustrate the applications, two case studies are presented with real experimental data sets collected at the Linac Coherent Light Source.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ma, S.Liu, H.2016-03-18doi:10.1107/S1600576716004337International Union of CrystallographyThis article describes software for fast model reconstruction from small-angle scattering data, providing real-time feedback on experiments.enX-RAY FREE-ELECTRON LASERS; XFELS; SMALL-ANGLE X-RAY SCATTERING; PROTEIN STRUCTURE; SINGLE-PARTICLE IMAGING; COMPUTER PROGRAMSX-ray free-electron lasers generate intense femtosecond X-ray pulses, so that high-resolution structure determination becomes feasible from noncrystalline samples, such as single particles or single molecules. At the moment, the orientation of sample particles cannot be precisely controlled, and consequently the unknown orientation needs to be recovered using computational algorithms. This delays the model reconstruction until all the scattering patterns have been re-oriented, which often entails a long elapse of time and until the completion of the experiment. The scattering patterns from single particles or multiple particles can be summed to form a virtual powder diffraction pattern, and the low-resolution region, corresponding to the small-angle X-ray scattering (SAXS) regime, can be analysed using existing SAXS methods. This work presents a pipeline that converts single-particle data sets into SAXS data, from which real-time model reconstruction is achieved using the model retrieval approach implemented in the software package SASTBX [Liu, Hexemer & Zwart (2012). J. Appl. Cryst. 45, 587–593]. To illustrate the applications, two case studies are presented with real experimental data sets collected at the Linac Coherent Light Source.text/htmlFacilitating model reconstruction for single-particle scattering using small-angle X-ray scattering methodsThis article will form part of a virtual special issue of the journal on free-electron laser software.text2492016-03-18Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs665med@iucr.orgApril 20166711600-5767Structure of nanocrystalline calcium silicate hydrates: insights from X-ray diffraction, synchrotron X-ray absorption and nuclear magnetic resonancehttp://scripts.iucr.org/cgi-bin/paper?po5053
The structure of nanocrystalline calcium silicate hydrates (C–S–H) having Ca/Si ratios ranging between 0.57 ± 0.05 and 1.47 ± 0.04 was studied using an electron probe micro-analyser, powder X-ray diffraction, 29Si magic angle spinning NMR, and Fourier-transform infrared and synchrotron X-ray absorption spectroscopies. All samples can be described as nanocrystalline and defective tobermorite. At low Ca/Si ratio, the Si chains are defect free and the Si Q3 and Q2 environments account, respectively, for up to 40.2 ± 1.5% and 55.6 ± 3.0% of the total Si, with part of the Q3 Si being attributable to remnants of the synthesis reactant. As the Ca/Si ratio increases up to 0.87 ± 0.02, the Si Q3 environment decreases down to 0 and is preferentially replaced by the Q2 environment, which reaches 87.9 ± 2.0%. At higher ratios, Q2 decreases down to 32.0 ± 7.6% for Ca/Si = 1.38 ± 0.03 and is replaced by the Q1 environment, which peaks at 68.1 ± 3.8%. The combination of X-ray diffraction and NMR allowed capturing the depolymerization of Si chains as well as a two-step variation in the layer-to-layer distance. This latter first increases from ∼11.3 Å (for samples having a Ca/Si ratio <∼0.6) up to 12.25 Å at Ca/Si = 0.87 ± 0.02, probably as a result of a weaker layer-to-layer connectivity, and then decreases down to 11 Å when the Ca/Si ratio reaches 1.38 ± 0.03. The decrease in layer-to-layer distance results from the incorporation of interlayer Ca that may form a Ca(OH)2-like structure, nanocrystalline and intermixed with C–S–H layers, at high Ca/Si ratios.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Grangeon, S.Claret, F.Roosz, C.Sato, T.Gaboreau, S.Linard, Y.2016-04-12doi:10.1107/S1600576716003885International Union of CrystallographyThe structure of nanocrystalline calcium silicates hydrates (C–S–H) having Ca/Si ratios ranging between 0.57 ± 0.05 and 1.47 ± 0.04 was studied. All samples are nanocrystalline and defective tobermorite. An increase of the Ca/Si ratio resulting from omission of bridging Si in the Si chains and incorporation of interlayer Ca was observed.enCALCIUM SILICATE HYDRATES; C-S-H; X-RAY DIFFRACTION; 29SI NMR; SYNCHROTRON X-RAY ABSORPTIONThe structure of nanocrystalline calcium silicate hydrates (C–S–H) having Ca/Si ratios ranging between 0.57 ± 0.05 and 1.47 ± 0.04 was studied using an electron probe micro-analyser, powder X-ray diffraction, 29Si magic angle spinning NMR, and Fourier-transform infrared and synchrotron X-ray absorption spectroscopies. All samples can be described as nanocrystalline and defective tobermorite. At low Ca/Si ratio, the Si chains are defect free and the Si Q3 and Q2 environments account, respectively, for up to 40.2 ± 1.5% and 55.6 ± 3.0% of the total Si, with part of the Q3 Si being attributable to remnants of the synthesis reactant. As the Ca/Si ratio increases up to 0.87 ± 0.02, the Si Q3 environment decreases down to 0 and is preferentially replaced by the Q2 environment, which reaches 87.9 ± 2.0%. At higher ratios, Q2 decreases down to 32.0 ± 7.6% for Ca/Si = 1.38 ± 0.03 and is replaced by the Q1 environment, which peaks at 68.1 ± 3.8%. The combination of X-ray diffraction and NMR allowed capturing the depolymerization of Si chains as well as a two-step variation in the layer-to-layer distance. This latter first increases from ∼11.3 Å (for samples having a Ca/Si ratio <∼0.6) up to 12.25 Å at Ca/Si = 0.87 ± 0.02, probably as a result of a weaker layer-to-layer connectivity, and then decreases down to 11 Å when the Ca/Si ratio reaches 1.38 ± 0.03. The decrease in layer-to-layer distance results from the incorporation of interlayer Ca that may form a Ca(OH)2-like structure, nanocrystalline and intermixed with C–S–H layers, at high Ca/Si ratios.text/htmlStructure of nanocrystalline calcium silicate hydrates: insights from X-ray diffraction, synchrotron X-ray absorption and nuclear magnetic resonancetext3492016-04-12Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers771med@iucr.orgJune 20167831600-5767Accuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiationshttp://scripts.iucr.org/cgi-bin/paper?kc5030
This study reports 78 Rietveld quantitative phase analyses using Cu Kα1, Mo Kα1 and synchrotron radiations. Synchrotron powder diffraction has been used to validate the most challenging analyses. From the results for three series with increasing contents of an analyte (an inorganic crystalline phase, an organic crystalline phase and a glass), it is inferred that Rietveld analyses from high-energy Mo Kα1 radiation have slightly better accuracies than those obtained from Cu Kα1 radiation. This behaviour has been established from the results of the calibration graphics obtained through the spiking method and also from Kullback–Leibler distance statistic studies. This outcome is explained, in spite of the lower diffraction power for Mo radiation when compared to Cu radiation, as arising because of the larger volume tested with Mo and also because higher energy allows one to record patterns with fewer systematic errors. The limit of detection (LoD) and limit of quantification (LoQ) have also been established for the studied series. For similar recording times, the LoDs in Cu patterns, ∼0.2 wt%, are slightly lower than those derived from Mo patterns, ∼0.3 wt%. The LoQ for a well crystallized inorganic phase using laboratory powder diffraction was established to be close to 0.10 wt% in stable fits with good precision. However, the accuracy of these analyses was poor with relative errors near to 100%. Only contents higher than 1.0 wt% yielded analyses with relative errors lower than 20%.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767León-Reina, L.García-Maté, M.Álvarez-Pinazo, G.Santacruz, I.Vallcorba, O.De la Torre, A.G.Aranda, M.A.G.2016-04-12doi:10.1107/S1600576716003873International Union of CrystallographyThis work focuses on the comparison of Mo Kα1 and Cu Kα1 radiations for the Rietveld quantitative phase analysis of challenging crystalline mixtures including amorphous content determination. The quantifications have been carried out by using calibration curves with increasing amounts of a given phase. Mo Kα1 patterns were found to yield slightly more accurate analyses than those derived from Cu Kα1 radiation.enLIMIT OF QUANTIFICATION; SPIKING METHOD; HIGH-ENERGY LABORATORY X-RAY POWDER DIFFRACTIONThis study reports 78 Rietveld quantitative phase analyses using Cu Kα1, Mo Kα1 and synchrotron radiations. Synchrotron powder diffraction has been used to validate the most challenging analyses. From the results for three series with increasing contents of an analyte (an inorganic crystalline phase, an organic crystalline phase and a glass), it is inferred that Rietveld analyses from high-energy Mo Kα1 radiation have slightly better accuracies than those obtained from Cu Kα1 radiation. This behaviour has been established from the results of the calibration graphics obtained through the spiking method and also from Kullback–Leibler distance statistic studies. This outcome is explained, in spite of the lower diffraction power for Mo radiation when compared to Cu radiation, as arising because of the larger volume tested with Mo and also because higher energy allows one to record patterns with fewer systematic errors. The limit of detection (LoD) and limit of quantification (LoQ) have also been established for the studied series. For similar recording times, the LoDs in Cu patterns, ∼0.2 wt%, are slightly lower than those derived from Mo patterns, ∼0.3 wt%. The LoQ for a well crystallized inorganic phase using laboratory powder diffraction was established to be close to 0.10 wt% in stable fits with good precision. However, the accuracy of these analyses was poor with relative errors near to 100%. Only contents higher than 1.0 wt% yielded analyses with relative errors lower than 20%.text/htmlAccuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiationstext3492016-04-12Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers722med@iucr.orgJune 20167351600-5767Element-specific structural analysis of Si/B4C using resonant X-ray reflectivity. Corrigendum http://scripts.iucr.org/cgi-bin/paper?me0614
Errors in the article by Nayak, Pradhan & Lodha [J. Appl. Cryst. (2015), 48, 786–796] are corrected.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Nayak, M.Pradhan, P.C.Lodha, G.S.2016-03-08doi:10.1107/S1600576716003824International Union of CrystallographyErrors in the article by Nayak, Pradhan & Lodha [J. Appl. Cryst. (2015), 48, 786–796] are corrected.enINTERFACE STRUCTURE; COMPOSITION AND IMPURITIES; RESONANT X-RAY REFLECTIVITYErrors in the article by Nayak, Pradhan & Lodha [J. Appl. Cryst. (2015), 48, 786–796] are corrected.text/htmlElement-specific structural analysis of Si/B4C using resonant X-ray reflectivity. Corrigendum text2492016-03-08Journal of Applied CrystallographyCopyright (c) 2016 International Union of Crystallography1600-5767addenda and errata715med@iucr.orgApril 20167161600-5767Multigrain indexing of unknown multiphase materialshttp://scripts.iucr.org/cgi-bin/paper?pd5064
A multigrain indexing algorithm for use with samples comprising an arbitrary number of known or unknown phases is presented. No a priori crystallographic knowledge is required. The algorithm applies to data acquired with a monochromatic beam and a conventional two-dimensional detector for diffraction. Initially, candidate grains are found by searching for crystallographic planes, using a Dirac comb convoluted with a box function as a filter. Next, candidate grains are validated and the unit cell is optimized. The algorithm is validated by simulations. Simulations of 500 cementite grains and ∼100 reflections per grain resulted in 99.2% of all grains being indexed correctly and 99.5% of the reflections becoming associated with the right grain. Simulations with 200 grains associated with four mineral phases and 50–700 reflections per grain resulted in 99.9% of all grains being indexed correctly and 99.9% of the reflections becoming associated with the right grain. The main limitation is in terms of overlap of diffraction spots and computing time. Potential areas of use include three-dimensional grain mapping, structural solution and refinement studies of complex samples, and studies of dilute phases.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Wejdemann, C.Poulsen, H.F.2016-03-24doi:10.1107/S1600576716003691International Union of CrystallographyA multigrain indexing algorithm for use with samples comprising an arbitrary number of known or unknown phases is presented.enINDEXING; MULTIGRAIN CRYSTALLOGRAPHY; THREE-DIMENSIONAL X-RAY DIFFRACTION MICROSCOPY; 3DXRDA multigrain indexing algorithm for use with samples comprising an arbitrary number of known or unknown phases is presented. No a priori crystallographic knowledge is required. The algorithm applies to data acquired with a monochromatic beam and a conventional two-dimensional detector for diffraction. Initially, candidate grains are found by searching for crystallographic planes, using a Dirac comb convoluted with a box function as a filter. Next, candidate grains are validated and the unit cell is optimized. The algorithm is validated by simulations. Simulations of 500 cementite grains and ∼100 reflections per grain resulted in 99.2% of all grains being indexed correctly and 99.5% of the reflections becoming associated with the right grain. Simulations with 200 grains associated with four mineral phases and 50–700 reflections per grain resulted in 99.9% of all grains being indexed correctly and 99.9% of the reflections becoming associated with the right grain. The main limitation is in terms of overlap of diffraction spots and computing time. Potential areas of use include three-dimensional grain mapping, structural solution and refinement studies of complex samples, and studies of dilute phases.text/htmlMultigrain indexing of unknown multiphase materialstext2492016-03-24Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers616med@iucr.orgApril 20166211600-5767Jan T. Bonarski (1957–2016)http://scripts.iucr.org/cgi-bin/paper?es0416
Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Chateigner, D.Baudin, T.Esling, C.Morawiec, A.Solas, D.2016-03-01doi:10.1107/S1600576716003368International Union of CrystallographyObituary for Jan T. Bonarski.enOBITUARYtext/htmlJan T. Bonarski (1957–2016)text2492016-03-01Journal of Applied CrystallographyCopyright (c) 2016 International Union of Crystallography1600-5767crystallographers717med@iucr.orgApril 20167171600-5767Aurore: new software for neutron reflectivity data analysis. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?rg9094
An incorrect statement in the paper by Gerelli [J. Appl. Cryst. (2016), 49, 330–339] is corrected.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Gerelli, Y.2016-02-16doi:10.1107/S1600576716002466International Union of CrystallographyAn incorrect statement in the paper by Gerelli [J. Appl. Cryst. (2016), 49, 330–339] is corrected.enNEUTRON REFLECTIVITY DATA ANALYSIS; COMPUTER PROGRAMSAn incorrect statement in the paper by Gerelli [J. Appl. Cryst. (2016), 49, 330–339] is corrected.text/htmlAurore: new software for neutron reflectivity data analysis. Corrigendumtext2492016-02-16Journal of Applied CrystallographyCopyright (c) 2016 International Union of Crystallography1600-5767addenda and errata712med@iucr.orgApril 20167121600-5767Analyzing diffuse scattering with supercomputers. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?kc5034
Errors in the paper by Michels-Clark, Lynch, Hoffmann, Hauser, Weber, Harrison & Bürgi [J. Appl. Cryst. (2013), 46, 1616–1625] are corrected.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Michels-Clark, T.M.Lynch, V.E.Hoffmann, C.M.Hauser, J.Weber, T.Harrison, R.Bürgi, H.B.2016-03-01doi:10.1107/S1600576716002077International Union of CrystallographyErrors in the paper by Michels-Clark, Lynch, Hoffmann, Hauser, Weber, Harrison & Bürgi [J. Appl. Cryst. (2013), 46, 1616–1625] are corrected.enDIFFUSE SCATTERING; QUANTITATIVE ANALYSIS; SUPERCOMPUTERSErrors in the paper by Michels-Clark, Lynch, Hoffmann, Hauser, Weber, Harrison & Bürgi [J. Appl. Cryst. (2013), 46, 1616–1625] are corrected.text/htmlAnalyzing diffuse scattering with supercomputers. Corrigendumtext2492016-03-01Journal of Applied CrystallographyCopyright (c) 2016 International Union of Crystallography1600-5767addenda and errata713med@iucr.orgApril 20167141600-5767Magnetic field-dependent spin structures of nanocrystalline holmiumhttp://scripts.iucr.org/cgi-bin/paper?to5123
The results are reported of magnetic field-dependent neutron diffraction experiments on polycrystalline inert-gas condensed holmium with a nanometre crystallite size (D = 33 nm). At T = 50 K, no evidence is found for the existence of helifan(3/2) or helifan(2) structures for the nanocrystalline sample, in contrast with results reported in the literature for the single crystal. Instead, when the applied field H is increased, the helix pattern transforms progressively, most likely into a fan structure. It is the component of H which acts on the basal-plane spins of a given nanocrystallite that drives the disappearance of the helix; for nanocrystalline Ho, this field is about 1.3 T, and it is related to a characteristic kink in the virgin magnetization curve. For a coarse-grained Ho sample, concomitant with the destruction of the helix phase, the emergence of an unusual angular anisotropy (streak pattern) and the appearance of novel spin structures are observed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Szary, P.Kaiser, D.Bick, J.-P.Lott, D.Heinemann, A.Dewhurst, C.Birringer, R.Michels, A.2016-03-08doi:10.1107/S1600576716001898International Union of CrystallographyNeutron diffraction experiments on nanocrystalline holmium suggest the absence of helifan(3/2) and helifan(2) structures at 50 K.enNEUTRON DIFFRACTION; SPIN STRUCTURES; RARE EARTH METALS; MAGNETIC MATERIALS; NANOCRYSTALLINE HOLMIUMThe results are reported of magnetic field-dependent neutron diffraction experiments on polycrystalline inert-gas condensed holmium with a nanometre crystallite size (D = 33 nm). At T = 50 K, no evidence is found for the existence of helifan(3/2) or helifan(2) structures for the nanocrystalline sample, in contrast with results reported in the literature for the single crystal. Instead, when the applied field H is increased, the helix pattern transforms progressively, most likely into a fan structure. It is the component of H which acts on the basal-plane spins of a given nanocrystallite that drives the disappearance of the helix; for nanocrystalline Ho, this field is about 1.3 T, and it is related to a characteristic kink in the virgin magnetization curve. For a coarse-grained Ho sample, concomitant with the destruction of the helix phase, the emergence of an unusual angular anisotropy (streak pattern) and the appearance of novel spin structures are observed.text/htmlMagnetic field-dependent spin structures of nanocrystalline holmiumtext2492016-03-08Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers533med@iucr.orgApril 20165381600-5767Expanding Lorentz and spectrum corrections to large volumes of reciprocal space for single-crystal time-of-flight neutron diffractionhttp://scripts.iucr.org/cgi-bin/paper?fs5119
Evidence is mounting that potentially exploitable properties of technologically and chemically interesting crystalline materials are often attributable to local structure effects, which can be observed as modulated diffuse scattering (mDS) next to Bragg diffraction (BD). BD forms a regular sparse grid of intense discrete points in reciprocal space. Traditionally, the intensity of each Bragg peak is extracted by integration of each individual reflection first, followed by application of the required corrections. In contrast, mDS is weak and covers expansive volumes of reciprocal space close to, or between, Bragg reflections. For a representative measurement of the diffuse scattering, multiple sample orientations are generally required, where many points in reciprocal space are measured multiple times and the resulting data are combined. The common post-integration data reduction method is not optimal with regard to counting statistics. A general and inclusive data processing method is needed. In this contribution, a comprehensive data analysis approach is introduced to correct and merge the full volume of scattering data in a single step, while correctly accounting for the statistical weight of the individual measurements. Development of this new approach required the exploration of a data treatment and correction protocol that includes the entire collected reciprocal space volume, using neutron time-of-flight or wavelength-resolved data collected at TOPAZ at the Spallation Neutron Source at Oak Ridge National Laboratory.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Michels-Clark, T.M.Savici, A.T.Lynch, V.E.Wang, X.P.Hoffmann, C.M.2016-03-01doi:10.1107/S1600576716001369International Union of CrystallographyExtraction of structure factor amplitudes from total scattering (Bragg + diffuse diffraction) data for local structure modeling remains a significant challenge, especially when considering time-of-flight measurements. Individual intensity contributions carry different statistical weights, with associated distinctive effects on data summation and correction. A comprehensive, statistically improved data analysis approach to correct and scale the complete volume of reciprocal space data in one step is described.enMODULATED DIFFUSE SCATTERING; LOCAL STRUCTURE MODELING; LORENTZ AND SPECTRUM CORRECTIONS; SINGLE-CRYSTAL TIME-OF-FLIGHT NEUTRON DIFFRACTIONEvidence is mounting that potentially exploitable properties of technologically and chemically interesting crystalline materials are often attributable to local structure effects, which can be observed as modulated diffuse scattering (mDS) next to Bragg diffraction (BD). BD forms a regular sparse grid of intense discrete points in reciprocal space. Traditionally, the intensity of each Bragg peak is extracted by integration of each individual reflection first, followed by application of the required corrections. In contrast, mDS is weak and covers expansive volumes of reciprocal space close to, or between, Bragg reflections. For a representative measurement of the diffuse scattering, multiple sample orientations are generally required, where many points in reciprocal space are measured multiple times and the resulting data are combined. The common post-integration data reduction method is not optimal with regard to counting statistics. A general and inclusive data processing method is needed. In this contribution, a comprehensive data analysis approach is introduced to correct and merge the full volume of scattering data in a single step, while correctly accounting for the statistical weight of the individual measurements. Development of this new approach required the exploration of a data treatment and correction protocol that includes the entire collected reciprocal space volume, using neutron time-of-flight or wavelength-resolved data collected at TOPAZ at the Spallation Neutron Source at Oak Ridge National Laboratory.text/htmlExpanding Lorentz and spectrum corrections to large volumes of reciprocal space for single-crystal time-of-flight neutron diffractiontext2492016-03-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers497med@iucr.orgApril 20165061600-5767Interlaced X-ray diffraction computed tomographyhttp://scripts.iucr.org/cgi-bin/paper?nb5168
An X-ray diffraction computed tomography data-collection strategy that allows, post experiment, a choice between temporal and spatial resolution is reported. This strategy enables time-resolved studies on comparatively short timescales, or alternatively allows for improved spatial resolution if the system under study, or components within it, appear to be unchanging. The application of the method for studying an Mn–Na–W/SiO2 fixed-bed reactor in situ is demonstrated. Additionally, the opportunities to improve the data-collection strategy further, enabling post-collection tuning between statistical, temporal and spatial resolutions, are discussed. In principle, the interlaced scanning approach can also be applied to other pencil-beam tomographic techniques, like X-ray fluorescence computed tomography, X-ray absorption fine structure computed tomography, pair distribution function computed tomography and tomographic scanning transmission X-ray microscopy.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Vamvakeros, A.Jacques, S.D.M.Di Michiel, M.Senecal, P.Middelkoop, V.Cernik, R.J.Beale, A.M.2016-03-01doi:10.1107/S160057671600131XInternational Union of CrystallographyA new data-collection strategy for X­ray diffraction computed tomography experiments is presented that allows, post experiment, a choice between temporal and spatial resolution.enX-RAY DIFFRACTION COMPUTED TOMOGRAPHY; XRD-CT; CHEMICAL TOMOGRAPHY; HYPERSPECTRAL TOMOGRAPHYAn X-ray diffraction computed tomography data-collection strategy that allows, post experiment, a choice between temporal and spatial resolution is reported. This strategy enables time-resolved studies on comparatively short timescales, or alternatively allows for improved spatial resolution if the system under study, or components within it, appear to be unchanging. The application of the method for studying an Mn–Na–W/SiO2 fixed-bed reactor in situ is demonstrated. Additionally, the opportunities to improve the data-collection strategy further, enabling post-collection tuning between statistical, temporal and spatial resolutions, are discussed. In principle, the interlaced scanning approach can also be applied to other pencil-beam tomographic techniques, like X-ray fluorescence computed tomography, X-ray absorption fine structure computed tomography, pair distribution function computed tomography and tomographic scanning transmission X-ray microscopy.text/htmlInterlaced X-ray diffraction computed tomographytext2492016-03-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers485med@iucr.orgApril 20164961600-5767Orientation relationship of eutectoid FeAl and FeAl2http://scripts.iucr.org/cgi-bin/paper?kc5028
Fe–Al alloys in the aluminium range of 55–65 at.% exhibit a lamellar microstructure of B2-ordered FeAl and triclinic FeAl2, which is caused by a eutectoid decomposition of the high-temperature Fe5Al8 phase, the so-called ∊ phase. The orientation relationship of FeAl and FeAl2 has previously been studied by Bastin et al. [J. Cryst. Growth (1978), 43, 745] and Hirata et al. [Philos. Mag. Lett. (2008), 88, 491]. Since both results are based on different crystallographic data regarding FeAl2, the data are re-evaluated with respect to a recent re-determination of the FeAl2 phase provided by Chumak et al. [Acta Cryst. (2010), C66, i87]. It is found that both orientation relationships match subsequent to a rotation operation of 180° about a 〈112〉 crystallographic axis of FeAl or by applying the inversion symmetry of the FeAl2 crystal structure as suggested by the Chumak data set. Experimental evidence for the validity of the previously determined orientation relationships was found in as-cast fully lamellar material (random texture) as well as directionally solidified material (∼〈110〉FeAl || solidification direction) by means of orientation imaging microscopy and global texture measurements. In addition, a preferential interface between FeAl and FeAl2 was identified by means of trace analyses using cross sectioning with a focused ion beam. On the basis of these habit planes the orientation relationship between the two phases can be described by ({\overline 1}01)FeAl || (114)_{{\rm FeAl}_2}^{\rm Chumak} and [111]FeAl || [1\overline{1}0]_{{\rm Fe Al}_2}^{\rm Chumak}. There is no evidence for twinning within FeAl lamellae or alternating orientations of FeAl lamellae. Based on the determined orientation and interface data, an atomistic model of the structure relationship of Fe5Al8, FeAl and FeAl2 in the vicinity of the eutectoid decomposition is derived. This model is analysed with respect to the strain which has to be accommodated at the interface of FeAl and FeAl2.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Scherf, A.Kauffmann, A.Kauffmann-Weiss, S.Scherer, T.Li, X.Stein, F.Heilmaier, M.2016-02-24doi:10.1107/S1600576716000911International Union of CrystallographyThe orientation relationship and interface plane of eutectoid FeAl and FeAl2 lamellae are investigated in detail and a crystallographic model is proposed.enIRON ALUMINIDES; EUTECTOID DECOMPOSITION; ELECTRON BACKSCATTER DIFFRACTION; INTERFACESFe–Al alloys in the aluminium range of 55–65 at.% exhibit a lamellar microstructure of B2-ordered FeAl and triclinic FeAl2, which is caused by a eutectoid decomposition of the high-temperature Fe5Al8 phase, the so-called ∊ phase. The orientation relationship of FeAl and FeAl2 has previously been studied by Bastin et al. [J. Cryst. Growth (1978), 43, 745] and Hirata et al. [Philos. Mag. Lett. (2008), 88, 491]. Since both results are based on different crystallographic data regarding FeAl2, the data are re-evaluated with respect to a recent re-determination of the FeAl2 phase provided by Chumak et al. [Acta Cryst. (2010), C66, i87]. It is found that both orientation relationships match subsequent to a rotation operation of 180° about a 〈112〉 crystallographic axis of FeAl or by applying the inversion symmetry of the FeAl2 crystal structure as suggested by the Chumak data set. Experimental evidence for the validity of the previously determined orientation relationships was found in as-cast fully lamellar material (random texture) as well as directionally solidified material (∼〈110〉FeAl || solidification direction) by means of orientation imaging microscopy and global texture measurements. In addition, a preferential interface between FeAl and FeAl2 was identified by means of trace analyses using cross sectioning with a focused ion beam. On the basis of these habit planes the orientation relationship between the two phases can be described by ({\overline 1}01)FeAl || (114)_{{\rm FeAl}_2}^{\rm Chumak} and [111]FeAl || [1\overline{1}0]_{{\rm Fe Al}_2}^{\rm Chumak}. There is no evidence for twinning within FeAl lamellae or alternating orientations of FeAl lamellae. Based on the determined orientation and interface data, an atomistic model of the structure relationship of Fe5Al8, FeAl and FeAl2 in the vicinity of the eutectoid decomposition is derived. This model is analysed with respect to the strain which has to be accommodated at the interface of FeAl and FeAl2.text/htmlOrientation relationship of eutectoid FeAl and FeAl2text2492016-02-24Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers442med@iucr.orgApril 20164491600-5767The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlineshttp://scripts.iucr.org/cgi-bin/paper?te5009
The Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. Sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Russi, S.Song, J.McPhillips, S.E.Cohen, A.E.2016-02-24doi:10.1107/S1600576716000649International Union of CrystallographyThe Structural Molecular Biology group at SSRL has upgraded its crystal mounting robot (SAM) to enable a sample pin exchange time of approximately 25 s during automated screening of samples.enAUTOMATED CRYSTAL MOUNTING; HIGH-THROUGHPUT SAMPLE EXCHANGE; SAMPLE EXCHANGE ROBOT; SYNCHROTRON ROBOTICS; PROTEIN CRYSTALLOGRAPHY; REMOTE ACCESS; CRYO-CRYSTALLOGRAPHYThe Stanford Automated Mounter System, a system for mounting and dismounting cryo-cooled crystals, has been upgraded to increase the throughput of samples on the macromolecular crystallography beamlines at the Stanford Synchrotron Radiation Lightsource. This upgrade speeds up robot maneuvers, reduces the heating/drying cycles, pre-fetches samples and adds an air-knife to remove frost from the gripper arms. Sample pin exchange during automated crystal quality screening now takes about 25 s, five times faster than before this upgrade.text/htmlThe Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlinestext2492016-02-24Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767cryocrystallography papers622med@iucr.orgApril 20166261600-5767Extension of the sasCIF format and its applications for data processing and depositionhttp://scripts.iucr.org/cgi-bin/paper?aj5271
Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and provide independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. This update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Kachala, M.Westbrook, J.Svergun, D.2016-02-01doi:10.1107/S1600576715024942International Union of CrystallographyAn extension of the sasCIF format is intended for representation, storage and exchange of SAS data and SAS-based models. Open-source sasCIFtools are developed for convenient data conversion, and for deposition into and retrieval from databases and data-processing pipelines.enSASCIF; CIF; SMALL-ANGLE SCATTERING; COMPUTER PROGRAMSRecent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and provide independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. This update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.text/htmlExtension of the sasCIF format and its applications for data processing and depositiontext1492016-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767CIF applications302med@iucr.orgFebruary 20163101600-5767X-ray nanodiffraction analysis of stress oscillations in a W thin film on through-silicon viahttp://scripts.iucr.org/cgi-bin/paper?nb5161
Synchrotron X-ray nanodiffraction is used to analyse residual stress distributions in a 200 nm-thick W film deposited on the scalloped inner wall of a through-silicon via. The diffraction data are evaluated using a novel dedicated methodology which allows the quantification of axial and tangential stress components under the condition that radial stresses are negligible. The results reveal oscillatory axial stresses in the range of ∼445–885 MPa, with a distribution that correlates well with the scallop wavelength and morphology, as well as nearly constant tangential stresses of ∼800 MPa. The discrepancy with larger stress values obtained from a finite-element model, as well as from a blanket W film, is attributed to the morphology and microstructural nature of the W film in the via.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Todt, J.Hammer, H.Sartory, B.Burghammer, M.Kraft, J.Daniel, R.Keckes, J.Defregger, S.2016-02-01doi:10.1107/S1600576715023419International Union of CrystallographyX-ray nanodiffraction is used to evaluate axial and tangential residual stress distributions in a W thin film deposited on the scalloped inner wall of a through-silicon via. The results reveal oscillatory stress distributions which correlate well with the scallop wavelength and morphology.enX-RAY NANODIFFRACTION; RESIDUAL STRESS; THROUGH-SILICON VIASynchrotron X-ray nanodiffraction is used to analyse residual stress distributions in a 200 nm-thick W film deposited on the scalloped inner wall of a through-silicon via. The diffraction data are evaluated using a novel dedicated methodology which allows the quantification of axial and tangential stress components under the condition that radial stresses are negligible. The results reveal oscillatory axial stresses in the range of ∼445–885 MPa, with a distribution that correlates well with the scallop wavelength and morphology, as well as nearly constant tangential stresses of ∼800 MPa. The discrepancy with larger stress values obtained from a finite-element model, as well as from a blanket W film, is attributed to the morphology and microstructural nature of the W film in the via.text/htmlX-ray nanodiffraction analysis of stress oscillations in a W thin film on through-silicon viatext1492016-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers182med@iucr.orgFebruary 20161871600-5767Analysis of small-angle X-ray scattering data in the presence of significant instrumental smearinghttp://scripts.iucr.org/cgi-bin/paper?pd5072
A laboratory-scale small-angle X-ray scattering instrument with pinhole collimation has been used to assess smearing effects due to instrumental resolution. A new, numerically efficient method to smear ideal model intensities is developed and presented. It allows for directly using measured profiles of isotropic but otherwise arbitrary beams in smearing calculations. Samples of low-polydispersity polymer spheres have been used to show that scattering data can in this way be quantitatively modeled even when there is substantial distortion due to instrumental resolution.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Bergenholtz, J.Ulama, J.Zackrisson Oskolkova, M.2016-02-01doi:10.1107/S1600576715023444International Union of CrystallographyA new, numerically efficient method has been developed to account for instrumental resolution effects on isotropic small-angle X-ray scattering with pinhole collimation.enSMALL-ANGLE X-RAY SCATTERING; PINHOLE COLLIMATION; INSTRUMENTAL SMEARING EFFECTSA laboratory-scale small-angle X-ray scattering instrument with pinhole collimation has been used to assess smearing effects due to instrumental resolution. A new, numerically efficient method to smear ideal model intensities is developed and presented. It allows for directly using measured profiles of isotropic but otherwise arbitrary beams in smearing calculations. Samples of low-polydispersity polymer spheres have been used to show that scattering data can in this way be quantitatively modeled even when there is substantial distortion due to instrumental resolution.text/htmlAnalysis of small-angle X-ray scattering data in the presence of significant instrumental smearingtext1492016-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers47med@iucr.orgFebruary 2016541600-5767SENJU: a new time-of-flight single-crystal neutron diffractometer at J-PARChttp://scripts.iucr.org/cgi-bin/paper?fs5124
SENJU is a new single-crystal time-of-flight neutron diffractometer installed at BL18 at the Materials and Life Science Experimental Facility of the Japan Accelerator Research Complex (J-PARC). The diffractometer was designed for precise crystal and magnetic structure analyses under multiple extreme sample environments such as low temperature, high pressure and high magnetic field, and for diffraction measurements of small single crystals down to 0.1 mm3 in volume. SENJU comprises three choppers, an elliptical shape straight supermirror guide, a vacuum sample chamber and 37 scintillator area detectors. The moderator-to-sample distance is 34.8 m, and the sample-to-detector distance is 800 mm. The wavelength of incident neutrons is 0.4–4.4 Å (first frame). Because short-wavelength neutrons are available and the large solid angle around the sample position is covered by the area detectors, a large reciprocal space can be simultaneously measured. Furthermore, the vacuum sample chamber and collimator have been designed to produce a very low background level. Thus, the measurement of a small single crystal is possible. As sample environment devices, a newly developed cryostat with a two-axis (ω and φ axes) goniometer and some extreme environment devices, e.g. a vertical-field magnet, high-temperature furnace and high-pressure cell, are available. The structure analysis of a sub-millimetre size (0.1 mm3) single organic crystal, taurine, and a magnetic structure analysis of the antiferromagnetic phase of MnF2 have been performed. These results demonstrate that SENJU can be a powerful tool to promote materials science research.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ohhara, T.Kiyanagi, R.Oikawa, K.Kaneko, K.Kawasaki, T.Tamura, I.Nakao, A.Hanashima, T.Munakata, K.Moyoshi, T.Kuroda, T.Kimura, H.Sakakura, T.Lee, C.-H.Takahashi, M.Ohshima, K.-Kiyotani, T.Noda, Y.Arai, M.2016-02-01doi:10.1107/S1600576715022943International Union of CrystallographySENJU, a time-of-flight Laue-type single-crystal neutron diffractometer, was developed at the Materials and Life Science Experimental Facility of the Japan Accelerator Research Complex (J-PARC). Molecular structure analysis of a sub-millimetre taurine crystal and magnetic structure analysis of an MnF2 crystal were performed to evaluate its performance.enTIME-OF-FLIGHT LAUE-TYPE SINGLE-CRYSTAL NEUTRON DIFFRACTOMETER; MLF/J-PARC; SUB-MILLIMETRE CRYSTALS; EXTREME SAMPLE ENVIRONMENTSSENJU is a new single-crystal time-of-flight neutron diffractometer installed at BL18 at the Materials and Life Science Experimental Facility of the Japan Accelerator Research Complex (J-PARC). The diffractometer was designed for precise crystal and magnetic structure analyses under multiple extreme sample environments such as low temperature, high pressure and high magnetic field, and for diffraction measurements of small single crystals down to 0.1 mm3 in volume. SENJU comprises three choppers, an elliptical shape straight supermirror guide, a vacuum sample chamber and 37 scintillator area detectors. The moderator-to-sample distance is 34.8 m, and the sample-to-detector distance is 800 mm. The wavelength of incident neutrons is 0.4–4.4 Å (first frame). Because short-wavelength neutrons are available and the large solid angle around the sample position is covered by the area detectors, a large reciprocal space can be simultaneously measured. Furthermore, the vacuum sample chamber and collimator have been designed to produce a very low background level. Thus, the measurement of a small single crystal is possible. As sample environment devices, a newly developed cryostat with a two-axis (ω and φ axes) goniometer and some extreme environment devices, e.g. a vertical-field magnet, high-temperature furnace and high-pressure cell, are available. The structure analysis of a sub-millimetre size (0.1 mm3) single organic crystal, taurine, and a magnetic structure analysis of the antiferromagnetic phase of MnF2 have been performed. These results demonstrate that SENJU can be a powerful tool to promote materials science research.text/htmlSENJU: a new time-of-flight single-crystal neutron diffractometer at J-PARCtext1492016-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers120med@iucr.orgFebruary 20161271600-5767Misfit-induced changes of lattice parameters in two-phase systems: coherent/incoherent precipitates in a matrixhttp://scripts.iucr.org/cgi-bin/paper?ks5483
Elastic accommodation of precipitation-induced or thermally induced misfit leads to lattice-parameter changes in crystalline multi-phase systems. Formulae for calculation of such misfit-induced lattice-parameter changes are presented for the aggregate (matrix + second-phase particles) and for the individual matrix and second phase, recognizing the occurrence of either coherent or incoherent diffraction by the matrix and second-phase particles. An overview and an (re)interpretation on the above basis is presented of published lattice-parameter data, obtained by X-ray diffraction analyses of aggregates of matrix plus second-phase particles. Examples for three types of systems consisting of a matrix with misfitting second-phase particles are dealt with, which differ in the origin of the misfit (precipitation or thermally induced) and in the type of diffraction (coherent or incoherent diffraction of matrix plus second-phase particles). The experimental data are shown to be in good to very good agreement with predictions according to the current treatment.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Akhlaghi, M.Steiner, T.Meka, S.R.Mittemeijer, E.J.2016-02-01doi:10.1107/S1600576715022608International Union of CrystallographyThe article discusses misfit-induced lattice-parameter changes in two-phase systems as exposed by coherent diffraction of the assembly or incoherent diffraction by the matrix and the second-phase particles.enLATTICE-PARAMETER CHANGE; PRECIPITATION-INDUCED MISFIT; THERMALLY INDUCED MISFIT; ELASTIC/PLASTIC MISFIT ACCOMMODATION; COHERENT/INCOHERENT DIFFRACTIONElastic accommodation of precipitation-induced or thermally induced misfit leads to lattice-parameter changes in crystalline multi-phase systems. Formulae for calculation of such misfit-induced lattice-parameter changes are presented for the aggregate (matrix + second-phase particles) and for the individual matrix and second phase, recognizing the occurrence of either coherent or incoherent diffraction by the matrix and second-phase particles. An overview and an (re)interpretation on the above basis is presented of published lattice-parameter data, obtained by X-ray diffraction analyses of aggregates of matrix plus second-phase particles. Examples for three types of systems consisting of a matrix with misfitting second-phase particles are dealt with, which differ in the origin of the misfit (precipitation or thermally induced) and in the type of diffraction (coherent or incoherent diffraction of matrix plus second-phase particles). The experimental data are shown to be in good to very good agreement with predictions according to the current treatment.text/htmlMisfit-induced changes of lattice parameters in two-phase systems: coherent/incoherent precipitates in a matrixtext1492016-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers69med@iucr.orgFebruary 2016771600-5767COD::CIF::Parser: an error-correcting CIF parser for the Perl languagehttp://scripts.iucr.org/cgi-bin/paper?po5052
A syntax-correcting CIF parser, COD::CIF::Parser, is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser, the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Merkys, A.Vaitkus, A.Butkus, J.Okulič-Kazarinas, M.Kairys, V.Gražulis, S.2016-02-01doi:10.1107/S1600576715022396International Union of CrystallographyA syntax-correcting CIF parser, COD::CIF::Parser, is described that can parse CIF 1.1 files and accurately report the position and nature of the discovered syntactic problems while automatically correcting the most common and the most obvious syntactic deficiencies.enCIF PARSERS; PERL; CRYSTALLOGRAPHY OPEN DATABASEA syntax-correcting CIF parser, COD::CIF::Parser, is presented that can parse CIF 1.1 files and accurately report the position and the nature of the discovered syntactic problems. In addition, the parser is able to automatically fix the most common and the most obvious syntactic deficiencies of the input files. Bindings for Perl, C and Python programming environments are available. Based on COD::CIF::Parser, the cod-tools package for manipulating the CIFs in the Crystallography Open Database (COD) has been developed. The cod-tools package has been successfully used for continuous updates of the data in the automated COD data deposition pipeline, and to check the validity of COD data against the IUCr data validation guidelines. The performance, capabilities and applications of different parsers are compared.text/htmlCOD::CIF::Parser: an error-correcting CIF parser for the Perl languagetext1492016-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767CIF applications292med@iucr.orgFebruary 20163011600-5767A portable general-purpose application programming interface for CIF 2.0http://scripts.iucr.org/cgi-bin/paper?aj5270
The CIF API is an application programming interface and accompanying reference implementation for reading and writing CIFs and manipulating CIF data, with support for all versions of CIF through CIF 2.0. It features full support for Unicode in data block and save frame codes, data names, and data values; flexible character encoding; CIF 2.0 List and Table data types; CIF version auto-detection; event-based parsing; and arbitrary-precision numeric values. The interface and implementation are written in portable C, and they have been successfully built and tested on Linux, OS X and Windows. The CIF API is open-source software, available for use under the GNU Lesser General Public License.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Bollinger, J.C.2016-02-01doi:10.1107/S1600576715021883International Union of CrystallographyA C-language application programming interface and implementation are described that enable software developers to readily incorporate CIF 2.0 (and earlier) support into their applications.enCIF; CIF 2.0; COMPUTER PROGRAMSThe CIF API is an application programming interface and accompanying reference implementation for reading and writing CIFs and manipulating CIF data, with support for all versions of CIF through CIF 2.0. It features full support for Unicode in data block and save frame codes, data names, and data values; flexible character encoding; CIF 2.0 List and Table data types; CIF version auto-detection; event-based parsing; and arbitrary-precision numeric values. The interface and implementation are written in portable C, and they have been successfully built and tested on Linux, OS X and Windows. The CIF API is open-source software, available for use under the GNU Lesser General Public License.text/htmlA portable general-purpose application programming interface for CIF 2.0text1492016-02-01Journal of Applied CrystallographyCopyright (c) 2016 International Union of Crystallography1600-5767CIF applications285med@iucr.orgFebruary 20162911600-5767Specification of the Crystallographic Information File format, version 2.0http://scripts.iucr.org/cgi-bin/paper?aj5269
Version 2.0 of the CIF format incorporates novel features implemented in STAR 2.0. Among these are an expanded character repertoire, new and more flexible forms for quoted data values, and new compound data types. The CIF 2.0 format is compared with both CIF 1.1 and STAR 2.0, and a formal syntax specification is provided.Copyright (c) 2016 International Union of Crystallographyurn:issn:1600-5767Bernstein, H.J.Bollinger, J.C.Brown, I.D.Gražulis, S.Hester, J.R.McMahon, B.Spadaccini, N.Westbrook, J.D.Westrip, S.P.2016-02-01doi:10.1107/S1600576715021871International Union of CrystallographyVersion 2.0 of the CIF format is described and a formal specification is provided.enCIF; CIF 2.0Version 2.0 of the CIF format incorporates novel features implemented in STAR 2.0. Among these are an expanded character repertoire, new and more flexible forms for quoted data values, and new compound data types. The CIF 2.0 format is compared with both CIF 1.1 and STAR 2.0, and a formal syntax specification is provided.text/htmlSpecification of the Crystallographic Information File format, version 2.0text1492016-02-01Journal of Applied CrystallographyCopyright (c) 2016 International Union of Crystallography1600-5767CIF applications277med@iucr.orgFebruary 20162841600-5767The same once again please: a pedagogical introduction to normalizershttp://scripts.iucr.org/cgi-bin/paper?to5126
Normalizers of space groups are extensively used in the solution of diverse tasks in structural crystallography. Yet, they are often considered an `esoteric' topic, seldom introduced in the education curriculum of a crystallographer. This paper presents a pedagogical introduction with special emphasis on their role in the equivalent description of crystal structures.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Nespolo, M.2015-11-28doi:10.1107/S1600576715020749International Union of CrystallographyAn intuitive introduction to normalizers of point and space groups is proposed, to make the beginner feel at home with this concept and its use in crystallography.enEQUIVALENT DESCRIPTION OF CRYSTAL STRUCTURES; NORMALIZERS; NORMAL SUBGROUPS; CONJUGATED SUBGROUPS; CRYSTALLOGRAPHIC EDUCATIONNormalizers of space groups are extensively used in the solution of diverse tasks in structural crystallography. Yet, they are often considered an `esoteric' topic, seldom introduced in the education curriculum of a crystallographer. This paper presents a pedagogical introduction with special emphasis on their role in the equivalent description of crystal structures.text/htmlThe same once again please: a pedagogical introduction to normalizerstext486Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-11-28teaching and education1600-5767med@iucr.org1600-5767Inside the bulk of magnetic nanocomposites: I am not what I amTitle quotation after Shakespeare (Othello I, 1).http://scripts.iucr.org/cgi-bin/paper?jo5015
http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Stuhrmann, H.B.2015-11-28doi:10.1107/S160057671502066XInternational Union of CrystallographyAn unexpected and not always easily discernible feature in the picture of magnetic neutron scattering is widening the outlook on micromagnetic architecture [Mettus & Michels (2015). J. Appl. Cryst. 48, 1437–1450]. enSMALL-ANGLE NEUTRON SCATTERING; CORRELATION FUNCTION; MICROMAGNETICS; MAGNETIC MATERIALStext/htmlInside the bulk of magnetic nanocomposites: I am not what I amTitle quotation after Shakespeare (Othello I, 1).text486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-28scientific commentaries1600-5767med@iucr.org1600-5767The equation of state of the Pmmn phase of NiSihttp://scripts.iucr.org/cgi-bin/paper?kc5022
The equation of state of the orthorhombic phase of NiSi with Pmmn symmetry has been determined at room temperature from synchrotron-based X-ray diffraction measurements of its lattice parameters, made in a diamond anvil cell. Measurements were performed up to 44 GPa, using Ne as the pressure medium and Au as the pressure standard. The resulting pressure–volume (P–V) data have been fitted with a Birch–Murnaghan equation of state of third order to yield V0 = 11.650 (7) Å3 atom−1, K0 = 162 (3) GPa and K0′ = 4.6 (2). In addition, P–V data have been collected on Ni53Si47 in the B20 structure using both Ne and He as the pressure media and Cu and Au as the pressure standards, also to 44 GPa. A fit using the same Birch–Murnaghan equation of state of third order yields V0 = 11.364 (6) Å3 atom−1, K0 = 171 (4) GPa and K0′ = 5.5 (3).http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Lord, O.T.Thomson, A.R.Wann, E.T.H.Wood, I.G.Dobson, D.P.Vocadlo, L.2015-11-28doi:10.1107/S1600576715020087International Union of CrystallographyThe room-temperature equations of state of NiSi with Pmmn symmetry and Ni53Si47 in the B20 structure have been determined to 50 GPa using a diamond anvil cell. The equations of state are compared with existing experimental data and ab initio simulations.enNISI; EQUATIONS OF STATE; HIGH PRESSURE; DIAMOND ANVIL CELLSThe equation of state of the orthorhombic phase of NiSi with Pmmn symmetry has been determined at room temperature from synchrotron-based X-ray diffraction measurements of its lattice parameters, made in a diamond anvil cell. Measurements were performed up to 44 GPa, using Ne as the pressure medium and Au as the pressure standard. The resulting pressure–volume (P–V) data have been fitted with a Birch–Murnaghan equation of state of third order to yield V0 = 11.650 (7) Å3 atom−1, K0 = 162 (3) GPa and K0′ = 4.6 (2). In addition, P–V data have been collected on Ni53Si47 in the B20 structure using both Ne and He as the pressure media and Cu and Au as the pressure standards, also to 44 GPa. A fit using the same Birch–Murnaghan equation of state of third order yields V0 = 11.364 (6) Å3 atom−1, K0 = 171 (4) GPa and K0′ = 5.5 (3).text/htmlThe equation of state of the Pmmn phase of NiSitext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-28research papers1600-5767med@iucr.org1600-5767Atomic disorder of Li0.5Ni0.5O thin films caused by Li doping: estimation from X-ray Debye–Waller factorshttp://scripts.iucr.org/cgi-bin/paper?rg5092
Cubic type room-temperature (RT) epitaxial Li0.5Ni0.5O and NiO thin films with [111] orientation grown on ultra-smooth sapphire (0001) substrates were examined using synchrotron-based thin-film X-ray diffraction. The 1\overline{1}1 and 2\overline{2}2 rocking curves including six respective equivalent reflections of the Li0.5Ni0.5O and NiO thin films were recorded. The RT B1 factor, which appears in the Debye–Waller factor, of a cubic Li0.5Ni0.5O thin film was estimated to be 1.8 (4) Å2 from its 1\overline{1}1 and 2\overline{2}2 reflections, even though the Debye model was originally derived on the basis of one cubic element. The corresponding Debye temperature is 281 (39) K. Furthermore, the B2 factor in the pseudo-Debye–Waller factor is proposed. This parameter, which is evaluated using one reflection, was also determined for the Li0.5Ni0.5O thin film by treating Li0.5Ni0.5O and NiO as ideal NaCl crystal structures. A structural parameter for the atomic disorder is introduced and evaluated. This parameter includes the combined effects of thermal vibration, interstitial atoms and defects caused by Li doping using the two Debye–Waller factors.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Yang, A.Sakata, O.Yamauchi, R.Kumara, L.S.R.Song, C.H.Katsuya, Y.Matsuda, A.Yoshimoto, M.2015-11-19doi:10.1107/S1600576715020002International Union of CrystallographyThe structures of room-temperature epitaxial Li0.5Ni0.5O and NiO thin films are compared. A structural parameter for the atomic disorder is discussed and evaluated using X-ray Debye–Waller factors.enATOMIC DISORDER; THIN FILMS; LI DOPING; DEBYE-WALLER FACTORSCubic type room-temperature (RT) epitaxial Li0.5Ni0.5O and NiO thin films with [111] orientation grown on ultra-smooth sapphire (0001) substrates were examined using synchrotron-based thin-film X-ray diffraction. The 1\overline{1}1 and 2\overline{2}2 rocking curves including six respective equivalent reflections of the Li0.5Ni0.5O and NiO thin films were recorded. The RT B1 factor, which appears in the Debye–Waller factor, of a cubic Li0.5Ni0.5O thin film was estimated to be 1.8 (4) Å2 from its 1\overline{1}1 and 2\overline{2}2 reflections, even though the Debye model was originally derived on the basis of one cubic element. The corresponding Debye temperature is 281 (39) K. Furthermore, the B2 factor in the pseudo-Debye–Waller factor is proposed. This parameter, which is evaluated using one reflection, was also determined for the Li0.5Ni0.5O thin film by treating Li0.5Ni0.5O and NiO as ideal NaCl crystal structures. A structural parameter for the atomic disorder is introduced and evaluated. This parameter includes the combined effects of thermal vibration, interstitial atoms and defects caused by Li doping using the two Debye–Waller factors.text/htmlAtomic disorder of Li0.5Ni0.5O thin films caused by Li doping: estimation from X-ray Debye–Waller factorstext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-19research papers1600-5767med@iucr.org1600-5767Morphology of crystalline–amorphous olefin block copolymers in solution characterized by small-angle neutron scattering and microscopyhttp://scripts.iucr.org/cgi-bin/paper?ge5017
The single-chain properties and self-assembly behavior in dilute solution of olefin block copolymers obtained by chain-shuttling technology and consisting of alternating crystallizable and amorphous ethylene/1-octene blocks were investigated by pinhole and focusing small-angle neutron scattering techniques, optical microscopy in bright-field and crossed-polarizer modes, and differential scanning calorimetry. The complex hydrocarbon soluble (precipitant free) macro-aggregates formed with decreasing temperature are characterized by spherulitic textures. The spherulites yield, on one hand, a morphology that depends on the chain structure properties and, on the other hand, multiple structural levels with a hierarchical organization that ranges from 10 Å up to tens of micrometres. This morphology displays peculiarities dictated by the polydisperse character of these materials.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Radulescu, A.Goerigk, G.Fetters, L.Richter, D.2015-11-19doi:10.1107/S1600576715019226International Union of CrystallographyThe multi-level structures and hierarchical morphologies formed by olefin block copolymers in dilute solution are characterized by pinhole and focusing small-angle neutron scattering techniques, optical microscopy in bright-field and crossed-polarizer modes, and differential scanning calorimetry.enBLOCK COPOLYMERS; CRYSTALLIZATION FROM SOLUTION; SMALL-ANGLE NEUTRON SCATTERING; OPTICAL MICROSCOPYThe single-chain properties and self-assembly behavior in dilute solution of olefin block copolymers obtained by chain-shuttling technology and consisting of alternating crystallizable and amorphous ethylene/1-octene blocks were investigated by pinhole and focusing small-angle neutron scattering techniques, optical microscopy in bright-field and crossed-polarizer modes, and differential scanning calorimetry. The complex hydrocarbon soluble (precipitant free) macro-aggregates formed with decreasing temperature are characterized by spherulitic textures. The spherulites yield, on one hand, a morphology that depends on the chain structure properties and, on the other hand, multiple structural levels with a hierarchical organization that ranges from 10 Å up to tens of micrometres. This morphology displays peculiarities dictated by the polydisperse character of these materials.text/htmlMorphology of crystalline–amorphous olefin block copolymers in solution characterized by small-angle neutron scattering and microscopytext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-19research papers1600-5767med@iucr.org1600-5767Tuning the instrument resolution using chopper and time of flight at the small-angle neutron scattering diffractometer KWS-2http://scripts.iucr.org/cgi-bin/paper?ge5015
Following demand from the user community regarding the possibility of improving the experimental resolution, the dedicated high-intensity/extended Q-range SANS diffractometer KWS-2 of the Jülich Centre for Neutron Science at the Heinz Maier-Leibnitz Center in Garching was equipped with a double-disc chopper with a variable opening slit window and time-of-flight (TOF) data acquisition option. The chopper used in concert with a dedicated high-intensity velocity selector enables the tuning at will of the wavelength resolution Δλ/λ within a broad range, from 20% (standard) down to 2%, in a convenient and safe manner following pre-planned or spontaneous decisions during the experiment. The new working mode is described in detail, and its efficiency is demonstrated on several standard samples with known properties and on a completely new crystallizable copolymer system, which were investigated using both the conventional (static) and TOF modes.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Radulescu, A.Székely, N.K.Polachowski, S.Leyendecker, M.Amann, M.Buitenhuis, J.Drochner, M.Engels, R.Hanslik, R.Kemmerling, G.Lindner, P.Papagiannopoulos, A.Pipich, V.Willner, L.Frielinghaus, H.Richter, D.2015-11-19doi:10.1107/S1600576715019019International Union of CrystallographyUsing a double-disc chopper with a variable slit opening in concert with a velocity selector and the time-of-flight data acquisition mode, controlled variation of the wavelength spread Δλ/λ between 2 and 20% has become routinely possible at the KWS-2 SANS diffractometer of the Jülich Centre for Neutron Science at the Heinz Maier-Leibnitz Center.enSMALL-ANGLE NEUTRON SCATTERING (SANS); TIME OF FLIGHT; WAVELENGTH SPREADFollowing demand from the user community regarding the possibility of improving the experimental resolution, the dedicated high-intensity/extended Q-range SANS diffractometer KWS-2 of the Jülich Centre for Neutron Science at the Heinz Maier-Leibnitz Center in Garching was equipped with a double-disc chopper with a variable opening slit window and time-of-flight (TOF) data acquisition option. The chopper used in concert with a dedicated high-intensity velocity selector enables the tuning at will of the wavelength resolution Δλ/λ within a broad range, from 20% (standard) down to 2%, in a convenient and safe manner following pre-planned or spontaneous decisions during the experiment. The new working mode is described in detail, and its efficiency is demonstrated on several standard samples with known properties and on a completely new crystallizable copolymer system, which were investigated using both the conventional (static) and TOF modes.text/htmlTuning the instrument resolution using chopper and time of flight at the small-angle neutron scattering diffractometer KWS-2text486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-19research papers1600-5767med@iucr.org1600-5767Accurate strain determination from digital image correlation of Laue diffraction spotshttp://scripts.iucr.org/cgi-bin/paper?me0589
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Borbély, A.2015-11-10doi:10.1107/S1600576715018981International Union of CrystallographyA new analysis based on digital image correlation of Laue diffraction spots determines the elements of the deviatoric strain tensor with an accuracy of about 10−5.enDEVIATORIC ELASTIC STRAIN; LATTICE ORIENTATION; DIGITAL IMAGE CORRELATION; LAUE MICRODIFFRACTIONtext/htmlAccurate strain determination from digital image correlation of Laue diffraction spotstext486Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-11-10scientific commentaries1600-5767med@iucr.org1600-5767Logistic regression models to predict solvent accessible residues using sequence- and homology-based qualitative and quantitative descriptors applied to a domain-complete X-ray structure learning sethttp://scripts.iucr.org/cgi-bin/paper?aj5252
A working example of relative solvent accessibility (RSA) prediction for proteins is presented. Novel logistic regression models with various qualitative descriptors that include amino acid type and quantitative descriptors that include 20- and six-term sequence entropy have been built and validated. A domain-complete learning set of over 1300 proteins is used to fit initial models with various sequence homology descriptors as well as query residue qualitative descriptors. Homology descriptors are derived from BLASTp sequence alignments, whereas the RSA values are determined directly from the crystal structure. The logistic regression models are fitted using dichotomous responses indicating buried or accessible solvent, with binary classifications obtained from the RSA values. The fitted models determine binary predictions of residue solvent accessibility with accuracies comparable to other less computationally intensive methods using the standard RSA threshold criteria 20 and 25% as solvent accessible. When an additional non-homology descriptor describing Lobanov–Galzitskaya residue disorder propensity is included, incremental improvements in accuracy are achieved with 25% threshold accuracies of 76.12 and 74.79% for the Manesh-215 and CASP(8+9) test sets, respectively. Moreover, the described software and the accompanying learning and validation sets allow students and researchers to explore the utility of RSA prediction with simple, physically intuitive models in any number of related applications.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Nepal, R.Spencer, J.Bhogal, G.Nedunuri, A.Poelman, T.Kamath, T.Chung, E.Kantardjieff, K.Gottlieb, A.Lustig, B.2015-11-10doi:10.1107/S1600576715018531International Union of CrystallographyThis article describes the development, validation and application of simple logistic regression models for the prediction of solvent accessible residues in oligomer and non-oligomer sets using a domain-complete X-ray structure learning set.enRELATIVE SOLVENT ACCESSIBILITY PREDICTION; TEACHING; EDUCATIONA working example of relative solvent accessibility (RSA) prediction for proteins is presented. Novel logistic regression models with various qualitative descriptors that include amino acid type and quantitative descriptors that include 20- and six-term sequence entropy have been built and validated. A domain-complete learning set of over 1300 proteins is used to fit initial models with various sequence homology descriptors as well as query residue qualitative descriptors. Homology descriptors are derived from BLASTp sequence alignments, whereas the RSA values are determined directly from the crystal structure. The logistic regression models are fitted using dichotomous responses indicating buried or accessible solvent, with binary classifications obtained from the RSA values. The fitted models determine binary predictions of residue solvent accessibility with accuracies comparable to other less computationally intensive methods using the standard RSA threshold criteria 20 and 25% as solvent accessible. When an additional non-homology descriptor describing Lobanov–Galzitskaya residue disorder propensity is included, incremental improvements in accuracy are achieved with 25% threshold accuracies of 76.12 and 74.79% for the Manesh-215 and CASP(8+9) test sets, respectively. Moreover, the described software and the accompanying learning and validation sets allow students and researchers to explore the utility of RSA prediction with simple, physically intuitive models in any number of related applications.text/htmlLogistic regression models to predict solvent accessible residues using sequence- and homology-based qualitative and quantitative descriptors applied to a domain-complete X-ray structure learning settext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-10teaching and education1600-5767med@iucr.org1600-5767Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis programhttp://scripts.iucr.org/cgi-bin/paper?vg5031
Invariom partitioning and notation are used to estimate anisotropic hydrogen displacements for incorporation in crystallographic refinement models. Optimized structures of the generalized invariom database and their frequency computations provide the information required: frequencies are converted to internal atomic displacements and combined with the results of a TLS (translation–libration–screw) fit of experimental non-hydrogen anisotropic displacement parameters to estimate those of H atoms. Comparison with TLS+ONIOM and neutron diffraction results for four example structures where high-resolution X-ray and neutron data are available show that electron density transferability rules established in the invariom approach are also suitable for streamlining the transfer of atomic vibrations. A new segmented-body TLS analysis program called APD-Toolkit has been coded to overcome technical limitations of the established program THMA. The influence of incorporating hydrogen anisotropic displacement parameters on conventional refinement is assessed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Lübben, J.Bourhis, L.J.Dittrich, B.2015-11-10doi:10.1107/S1600576715018075International Union of CrystallographyA novel method and a new program for estimating anisotropic displacement parameters for H atoms are presented. Results are validated against molecular orbital computations and neutron diffraction data.enANISOTROPIC DISPLACEMENT PARAMETERS; GENERALIZED INVARIOM DATABASE; SEGMENTED RIGID-BODY ANALYSISInvariom partitioning and notation are used to estimate anisotropic hydrogen displacements for incorporation in crystallographic refinement models. Optimized structures of the generalized invariom database and their frequency computations provide the information required: frequencies are converted to internal atomic displacements and combined with the results of a TLS (translation–libration–screw) fit of experimental non-hydrogen anisotropic displacement parameters to estimate those of H atoms. Comparison with TLS+ONIOM and neutron diffraction results for four example structures where high-resolution X-ray and neutron data are available show that electron density transferability rules established in the invariom approach are also suitable for streamlining the transfer of atomic vibrations. A new segmented-body TLS analysis program called APD-Toolkit has been coded to overcome technical limitations of the established program THMA. The influence of incorporating hydrogen anisotropic displacement parameters on conventional refinement is assessed.text/htmlEstimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis programtext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-10research papers1600-5767med@iucr.org1600-5767Simultaneous high-resolution scanning Bragg contrast and ptychographic imaging of a single solar cell nanowirehttp://scripts.iucr.org/cgi-bin/paper?rg5093
Simultaneous scanning Bragg contrast and small-angle ptychographic imaging of a single solar cell nanowire are demonstrated, using a nanofocused hard X-ray beam and two detectors. The 2.5 µm-long nanowire consists of a single-crystal InP core of 190 nm diameter, coated with amorphous SiO2 and polycrystalline indium tin oxide. The nanowire was selected and aligned in real space using the small-angle scattering of the 140 × 210 nm X-ray beam. The orientation of the nanowire, as observed in small-angle scattering, was used to find the correct rotation for the Bragg condition. After alignment in real space and rotation, high-resolution (50 nm step) raster scans were performed to simultaneously measure the distribution of small-angle scattering and Bragg diffraction in the nanowire. Ptychographic reconstruction of the coherent small-angle scattering was used to achieve sub-beam spatial resolution. The small-angle scattering images, which are sensitive to the shape and the electron density of all parts of the nanowire, showed a homogeneous profile along the nanowire axis except at the thicker head region. In contrast, the scanning Bragg diffraction microscopy, which probes only the single-crystal InP core, revealed bending and crystalline inhomogeneity. Both systematic and non-systematic real-space movement of the nanowire were observed as it was rotated, which would have been difficult to reveal only from the Bragg scattering. These results demonstrate the advantages of simultaneously collecting and analyzing the small-angle scattering in Bragg diffraction experiments.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Wallentin, J.Wilke, R.N.Osterhoff, M.Salditt, T.2015-11-10doi:10.1107/S1600576715017975International Union of CrystallographySimultaneous Bragg diffraction and coherent small-angle scattering of a single solar cell nanowire is demonstrated, using a nanofocused hard X-ray beam and two detectors.enX-RAY DIFFRACTION; NANOWIRES; SOLAR CELLS; PTYCHOGRAPHYSimultaneous scanning Bragg contrast and small-angle ptychographic imaging of a single solar cell nanowire are demonstrated, using a nanofocused hard X-ray beam and two detectors. The 2.5 µm-long nanowire consists of a single-crystal InP core of 190 nm diameter, coated with amorphous SiO2 and polycrystalline indium tin oxide. The nanowire was selected and aligned in real space using the small-angle scattering of the 140 × 210 nm X-ray beam. The orientation of the nanowire, as observed in small-angle scattering, was used to find the correct rotation for the Bragg condition. After alignment in real space and rotation, high-resolution (50 nm step) raster scans were performed to simultaneously measure the distribution of small-angle scattering and Bragg diffraction in the nanowire. Ptychographic reconstruction of the coherent small-angle scattering was used to achieve sub-beam spatial resolution. The small-angle scattering images, which are sensitive to the shape and the electron density of all parts of the nanowire, showed a homogeneous profile along the nanowire axis except at the thicker head region. In contrast, the scanning Bragg diffraction microscopy, which probes only the single-crystal InP core, revealed bending and crystalline inhomogeneity. Both systematic and non-systematic real-space movement of the nanowire were observed as it was rotated, which would have been difficult to reveal only from the Bragg scattering. These results demonstrate the advantages of simultaneously collecting and analyzing the small-angle scattering in Bragg diffraction experiments.text/htmlSimultaneous high-resolution scanning Bragg contrast and ptychographic imaging of a single solar cell nanowiretext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-11-10research papers1600-5767med@iucr.org1600-5767Crystallographic Tool Box (CrysTBox): automated tools for transmission electron microscopists and crystallographershttp://scripts.iucr.org/cgi-bin/paper?nb5151
Three tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly, diffractGUI determines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly, ringGUI identifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. Both diffractGUI and ringGUI employ methods of computer vision for a fast, robust and accurate analysis. Thirdly, cellViewer is an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes. diffractGUI and cellViewer can be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly from DigitalMicrograph (Gatan Inc.).http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Klinger, M.Jäger, A.2015-10-21doi:10.1107/S1600576715017252International Union of CrystallographyThe CrysTBox software for electron diffraction analysis and visualization is presented. Among others, the software offers an automated zone axis determination using selected area diffraction, convergent beam diffraction and nanodiffraction patterns, ring diffraction evaluation, and interactive crystal visualization in both direct and reciprocal space.enELECTRON DIFFRACTION; AUTOMATED ANALYSIS; TRANSMISSION ELECTRON MICROSCOPY; HIGH-RESOLUTION TRANSMISSION ELECTRON MICROSCOPYThree tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly, diffractGUI determines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly, ringGUI identifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. Both diffractGUI and ringGUI employ methods of computer vision for a fast, robust and accurate analysis. Thirdly, cellViewer is an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes. diffractGUI and cellViewer can be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly from DigitalMicrograph (Gatan Inc.).text/htmlCrystallographic Tool Box (CrysTBox): automated tools for transmission electron microscopists and crystallographerstext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-10-21computer programs1600-5767med@iucr.org1600-5767Crystallographic education in the 21st centuryhttp://scripts.iucr.org/cgi-bin/paper?gj5144
There are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Gražulis, S.Sarjeant, A.A.Moeck, P.Stone-Sundberg, J.Snyder, T.J.Kaminsky, W.Oliver, A.G.Stern, C.L.Dawe, L.N.Rychkov, D.A.Losev, E.A.Boldyreva, E.V.Tanski, J.M.Bernstein, J.Rabeh, W.M.Kantardjieff, K.A.2015-10-13doi:10.1107/S1600576715016830International Union of CrystallographyMethods and outcomes for teaching crystallography in graduate, post-graduate and secondary school environments are presented. This is an extended report based on the ideas presented in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly in Montreal.enTEACHING; EDUCATIONThere are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described.text/htmlCrystallographic education in the 21st centurytext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-10-13teaching and education1600-5767med@iucr.org1600-5767X-ray Scattering from Semiconductors and Other Materials. 3rd Ed. By Paul F. Fewster. Singapore: World Scientific Press, 2015. Pp. 493. Price GBP 65.00, USD 99.00. ISBN 9789814436922.http://scripts.iucr.org/cgi-bin/paper?xo0014
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Tanner, B.2015-09-20doi:10.1107/S1600576715016568International Union of CrystallographyenBOOK REVIEWS; X-RAY SCATTERINGtext/htmlX-ray Scattering from Semiconductors and Other Materials. 3rd Ed. By Paul F. Fewster. Singapore: World Scientific Press, 2015. Pp. 493. Price GBP 65.00, USD 99.00. ISBN 9789814436922.text485Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-09-201610book reviews1600-5767med@iucr.org16101600-5767A Rietveld refinement method for angular- and wavelength-dispersive neutron time-of-flight powder diffraction datahttp://scripts.iucr.org/cgi-bin/paper?pd5076
This paper introduces a two-dimensional extension of the well established Rietveld refinement method for modeling neutron time-of-flight powder diffraction data. The novel approach takes into account the variation of two parameters, diffraction angle 2θ and wavelength λ, to optimally adapt to the varying resolution function in diffraction experiments. By doing so, the refinement against angular- and wavelength-dispersive data gets rid of common data-reduction steps and also avoids the loss of high-resolution information typically introduced by integration. In a case study using a numerically simulated diffraction pattern of Rh0.81Fe3.19N taking into account the layout of the future POWTEX instrument, the profile function as parameterized in 2θ and λ is extracted. As a proof-of-concept, the resulting instrument parameterization is then utilized to perform a typical refinement of the angular- and wavelength-dispersive diffraction pattern of CuNCN, yielding excellent residuals within feasible computational efforts. Another proof-of-concept is carried out by applying the same approach to a real neutron diffraction data set of CuNCN obtained from the POWGEN instrument at the Spallation Neutron Source in Oak Ridge. The paper highlights the general importance of the novel approach for data analysis at neutron time-of-flight diffractometers and its possible inclusion within existing Rietveld software packages.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Jacobs, P.Houben, A.Schweika, W.Tchougréeff, A.L.Dronskowski, R.2015-10-13doi:10.1107/S1600576715016520International Union of CrystallographyThis paper introduces a novel approach to Rietveld refinements of two-dimensional angular- and wavelength-dispersive powder diffraction data as measured at time-of-flight neutron diffraction instruments. To do so, the authors' ansatz for diffraction data obtained from the POWGEN diffractometer has been verified, and furthermore its feasibility and benefit in simulations for the novel POWTEX instrument presently under construction are demonstrated.enRIETVELD REFINEMENT; NEUTRON DIFFRACTION; ANGULAR-DISPERSIVE; WAVELENGTH-DISPERSIVE; POWDER METHODS; VITESS; POWTEX; POWGENThis paper introduces a two-dimensional extension of the well established Rietveld refinement method for modeling neutron time-of-flight powder diffraction data. The novel approach takes into account the variation of two parameters, diffraction angle 2θ and wavelength λ, to optimally adapt to the varying resolution function in diffraction experiments. By doing so, the refinement against angular- and wavelength-dispersive data gets rid of common data-reduction steps and also avoids the loss of high-resolution information typically introduced by integration. In a case study using a numerically simulated diffraction pattern of Rh0.81Fe3.19N taking into account the layout of the future POWTEX instrument, the profile function as parameterized in 2θ and λ is extracted. As a proof-of-concept, the resulting instrument parameterization is then utilized to perform a typical refinement of the angular- and wavelength-dispersive diffraction pattern of CuNCN, yielding excellent residuals within feasible computational efforts. Another proof-of-concept is carried out by applying the same approach to a real neutron diffraction data set of CuNCN obtained from the POWGEN instrument at the Spallation Neutron Source in Oak Ridge. The paper highlights the general importance of the novel approach for data analysis at neutron time-of-flight diffractometers and its possible inclusion within existing Rietveld software packages.text/htmlA Rietveld refinement method for angular- and wavelength-dispersive neutron time-of-flight powder diffraction datatext486http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-10-13research papers1600-5767med@iucr.org1600-5767Representational analysis of extended disorder in atomistic ensembles derived from total scattering datahttp://scripts.iucr.org/cgi-bin/paper?po5036
With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atoms in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. This method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Neilson, J.R.McQueen, T.M.2015-09-20doi:10.1107/S1600576715016404International Union of CrystallographyRepresentational analysis is used to characterize correlated short-range order in large atomistic ensembles. This method, analogous to tight-binding methods, enables the extraction of relevant structural parameters in an orthogonal and local basis that permits robust statistical analysis of crystalline disorder.enEXTENDED DISORDER; ATOMISTIC ENSEMBLES; MODELING; PAIR DISTRIBUTION FUNCTION ANALYSISWith the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atoms in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. This method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.text/htmlRepresentational analysis of extended disorder in atomistic ensembles derived from total scattering datatext485http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-09-201560research papers1600-5767med@iucr.org15721600-5767SASfit: a tool for small-angle scattering data analysis using a library of analytical expressionshttp://scripts.iucr.org/cgi-bin/paper?vg5026
SASfit is one of the mature programs for small-angle scattering data analysis and has been available for many years. This article describes the basic data processing and analysis workflow along with recent developments in the SASfit program package (version 0.94.6). They include (i) advanced algorithms for reduction of oversampled data sets, (ii) improved confidence assessment in the optimized model parameters and (iii) a flexible plug-in system for custom user-provided models. A scattering function of a mass fractal model of branched polymers in solution is provided as an example for implementing a plug-in. The new SASfit release is available for major platforms such as Windows, Linux and MacOS. To facilitate usage, it includes comprehensive indexed documentation as well as a web-based wiki for peer collaboration and online videos demonstrating basic usage. The use of SASfit is illustrated by interpretation of the small-angle X-ray scattering curves of monomodal gold nanoparticles (NIST reference material 8011) and bimodal silica nanoparticles (EU reference material ERM-FD-102).http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Breßler, I.Kohlbrecher, J.Thünemann, A.F.2015-09-20doi:10.1107/S1600576715016544International Union of CrystallographyA computer program to perform small-angle X-ray and neutron scattering data evaluation is presented.enSMALL-ANGLE X-RAY SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; CURVE FITTING; NANOTECHNOLOGY; NANOPARTICLES; POLYMERSSASfit is one of the mature programs for small-angle scattering data analysis and has been available for many years. This article describes the basic data processing and analysis workflow along with recent developments in the SASfit program package (version 0.94.6). They include (i) advanced algorithms for reduction of oversampled data sets, (ii) improved confidence assessment in the optimized model parameters and (iii) a flexible plug-in system for custom user-provided models. A scattering function of a mass fractal model of branched polymers in solution is provided as an example for implementing a plug-in. The new SASfit release is available for major platforms such as Windows, Linux and MacOS. To facilitate usage, it includes comprehensive indexed documentation as well as a web-based wiki for peer collaboration and online videos demonstrating basic usage. The use of SASfit is illustrated by interpretation of the small-angle X-ray scattering curves of monomodal gold nanoparticles (NIST reference material 8011) and bimodal silica nanoparticles (EU reference material ERM-FD-102).text/htmlSASfit: a tool for small-angle scattering data analysis using a library of analytical expressionstext485http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-09-201587computer programs1600-5767med@iucr.org15981600-5767Topology and temperature dependence of the diffuse X-ray scattering in Na0.5Bi0.5TiO3 ferroelectric single crystalshttp://scripts.iucr.org/cgi-bin/paper?ks5473
The results of high-resolution measurements of the diffuse X-ray scattering produced by a perovskite-based Na0.5Bi0.5TiO3 ferroelectric single crystal between 40 and 620 K are reported. The study was designed as an attempt to resolve numerous controversies regarding the average structure of Na0.5Bi0.5TiO3, such as the mechanism of the phase transitions between the tetragonal, P4bm, and rhombohedral | monoclinic, R3c | Cc, space groups and the correlation between structural changes and macroscopic physical properties. The starting point was to search for any transformations of structural disorder in the temperature range of thermal depoling (420–480 K), where the average structure is known to remain unchanged. The intensity distribution around the {032} pseudocubic reflection was collected using a PILATUS 100K detector at the I16 beamline of the Diamond Light Source (UK). The data revealed previously unknown features of the diffuse scattering, including a system of dual asymmetric L-shaped diffuse scattering streaks. The topology, temperature dependence, and relationship between Bragg and diffuse intensities suggest the presence of complex microstructure in the low-temperature R3c | Cc phase. This microstructure may be formed by the persistence of the higher-temperature P4bm phase, built into a lower-temperature R3c | Cc matrix, accompanied by the related long-range strain fields. Finally, it is shown that a correlation between the temperature dependence of the X-ray scattering features and the temperature regime of thermal depoling is present.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Gorfman, S.Keeble, D.S.Bombardi, A.Thomas, P.A.2015-09-20doi:10.1107/S160057671501571XInternational Union of CrystallographyThe high-resolution temperature-dependent diffuse X-ray scattering from an Na0.5Bi0.5TiO3 perovskite-based single crystal is measured on the approach to the polymorphic phase transition. The previously unseen topological features of the diffuse scattering and their temperature evolution are reported.enSINGLE-CRYSTAL DIFFUSE X-RAY SCATTERING; LEAD-FREE FERROELECTRICS; HIGH-RESOLUTION X-RAY DIFFRACTION; PEROVSKITES; NA0.5BI0.5TIO3The results of high-resolution measurements of the diffuse X-ray scattering produced by a perovskite-based Na0.5Bi0.5TiO3 ferroelectric single crystal between 40 and 620 K are reported. The study was designed as an attempt to resolve numerous controversies regarding the average structure of Na0.5Bi0.5TiO3, such as the mechanism of the phase transitions between the tetragonal, P4bm, and rhombohedral | monoclinic, R3c | Cc, space groups and the correlation between structural changes and macroscopic physical properties. The starting point was to search for any transformations of structural disorder in the temperature range of thermal depoling (420–480 K), where the average structure is known to remain unchanged. The intensity distribution around the {032} pseudocubic reflection was collected using a PILATUS 100K detector at the I16 beamline of the Diamond Light Source (UK). The data revealed previously unknown features of the diffuse scattering, including a system of dual asymmetric L-shaped diffuse scattering streaks. The topology, temperature dependence, and relationship between Bragg and diffuse intensities suggest the presence of complex microstructure in the low-temperature R3c | Cc phase. This microstructure may be formed by the persistence of the higher-temperature P4bm phase, built into a lower-temperature R3c | Cc matrix, accompanied by the related long-range strain fields. Finally, it is shown that a correlation between the temperature dependence of the X-ray scattering features and the temperature regime of thermal depoling is present.text/htmlTopology and temperature dependence of the diffuse X-ray scattering in Na0.5Bi0.5TiO3 ferroelectric single crystalstext5482015-09-20Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1543med@iucr.orgOctober 201515501600-5767Scattering Methods in Complex Fluids. By Sow-Hsin Chen and Piero Tartaglia. Cambridge University Press, 2015. Pp. 400. Price (hardcover) GBP 75. ISBN 9780521883801.http://scripts.iucr.org/cgi-bin/paper?xo0020
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Teixeira, J.2015-08-18doi:10.1107/S1600576715014958International Union of CrystallographyenBOOK REVIEWS; SCATTERING METHODS; COMPLEX FLUIDStext/htmlScattering Methods in Complex Fluids. By Sow-Hsin Chen and Piero Tartaglia. Cambridge University Press, 2015. Pp. 400. Price (hardcover) GBP 75. ISBN 9780521883801.text485Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-08-181609book reviews1600-5767med@iucr.org16091600-5767Profex: a graphical user interface for the Rietveld refinement program BGMNhttp://scripts.iucr.org/cgi-bin/paper?kc5013
Profex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Doebelin, N.Kleeberg, R.2015-08-29doi:10.1107/S1600576715014685International Union of CrystallographyProfex is a platform-independent open-source graphical user interface for the Rietveld refinement program BGMN.enRIETVELD REFINEMENT; GRAPHICAL USER INTERFACE; BGMN; PROFEXProfex is a graphical user interface for the Rietveld refinement program BGMN. Its interface focuses on preserving BGMN's powerful and flexible scripting features by giving direct access to BGMN input files. Very efficient workflows for single or batch refinements are achieved by managing refinement control files and structure files, by providing dialogues and shortcuts for many operations, by performing operations in the background, and by providing import filters for CIF and XML crystal structure files. Refinement results can be easily exported for further processing. State-of-the-art graphical export of diffraction patterns to pixel and vector graphics formats allows the creation of publication-quality graphs with minimum effort. Profex reads and converts a variety of proprietary raw data formats and is thus largely instrument independent. Profex and BGMN are available under an open-source license for Windows, Linux and OS X operating systems.text/htmlProfex: a graphical user interface for the Rietveld refinement program BGMNtext485http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-08-291573computer programs1600-5767med@iucr.org15801600-5767Neutron Interferometry: Lessons in Experimental Quantum Mechanics, Wave–Particle Duality, and Entanglement. 2nd Ed. By Helmut Rauch and Samuel A. Werner. Oxford University Press, 2015. Price (hardcover) GBP 70. ISBN 978-0-19-871251-0.http://scripts.iucr.org/cgi-bin/paper?xo0017
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Silverman, M.P.2015-08-08doi:10.1107/S1600576715014582International Union of CrystallographyenBOOK REVIEW; NEUTRON INTERFEROMETRYtext/htmlNeutron Interferometry: Lessons in Experimental Quantum Mechanics, Wave–Particle Duality, and Entanglement. 2nd Ed. By Helmut Rauch and Samuel A. Werner. Oxford University Press, 2015. Price (hardcover) GBP 70. ISBN 978-0-19-871251-0.text485Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-08-08book reviews1600-5767med@iucr.org1600-5767Small-angle neutron scattering correlation functions of bulk magnetic materialshttp://scripts.iucr.org/cgi-bin/paper?aj5262
On the basis of the continuum theory of micromagnetics, the correlation function of the spin-misalignment small-angle neutron scattering cross section of bulk ferromagnets (e.g. elemental polycrystalline ferromagnets, soft and hard magnetic nanocomposites, nanoporous ferromagnets, or magnetic steels) is computed. For such materials, the spin disorder which is related to spatial variations in the saturation magnetization and magnetic anisotropy field results in strong spin-misalignment scattering dΣM/dΩ along the forward direction. When the applied magnetic field is perpendicular to the incoming neutron beam, the characteristics of dΣM/dΩ (e.g. the angular anisotropy on a two-dimensional detector or the asymptotic power-law exponent) are determined by the ratio of magnetic anisotropy field strength Hp to the jump ΔM in the saturation magnetization at internal interfaces. Here, the corresponding one- and two-dimensional real-space correlations are analyzed as a function of applied magnetic field, the ratio Hp/ΔM, the single-particle form factor and the particle volume fraction. Finally, the theoretical results for the correlation function are compared with experimental data on nanocrystalline cobalt and nickel.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Mettus, D.Michels, A.2015-08-29doi:10.1107/S1600576715013187International Union of CrystallographyOn the basis of the continuum theory of micromagnetics, the correlation function of the spin-misalignment small-angle neutron scattering cross section of bulk ferromagnets is computed and discussed.enSMALL-ANGLE NEUTRON SCATTERING; CORRELATION FUNCTION; MICROMAGNETICS; MAGNETIC MATERIALSOn the basis of the continuum theory of micromagnetics, the correlation function of the spin-misalignment small-angle neutron scattering cross section of bulk ferromagnets (e.g. elemental polycrystalline ferromagnets, soft and hard magnetic nanocomposites, nanoporous ferromagnets, or magnetic steels) is computed. For such materials, the spin disorder which is related to spatial variations in the saturation magnetization and magnetic anisotropy field results in strong spin-misalignment scattering dΣM/dΩ along the forward direction. When the applied magnetic field is perpendicular to the incoming neutron beam, the characteristics of dΣM/dΩ (e.g. the angular anisotropy on a two-dimensional detector or the asymptotic power-law exponent) are determined by the ratio of magnetic anisotropy field strength Hp to the jump ΔM in the saturation magnetization at internal interfaces. Here, the corresponding one- and two-dimensional real-space correlations are analyzed as a function of applied magnetic field, the ratio Hp/ΔM, the single-particle form factor and the particle volume fraction. Finally, the theoretical results for the correlation function are compared with experimental data on nanocrystalline cobalt and nickel.text/htmlSmall-angle neutron scattering correlation functions of bulk magnetic materialstext485http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-08-291437research papers1600-5767med@iucr.org14501600-5767Xtal-xplore-R: a graphical tool for exploring the residual function involved in crystal structure determinationhttp://scripts.iucr.org/cgi-bin/paper?po5037
This work presents Xtal-xplore-R, a tool dedicated to the visualization of two-dimensional cuts through the multidimensional crystallographic residual function. It imports arbitrary crystal structures, generates artificial diffraction data, and calculates and investigates the residual function in parameter space. The program serves two major purposes. Firstly, it is part of a more general project dealing with structure determination via global optimization techniques. In this context, the tool is being used to systematically analyse characteristic universal features of the target function (residual function) which can be used to develop appropriate problem-specific heuristic optimization algorithms. Secondly, Xtal-xplore-R is intended as a didactic tool to visualize how changes in atom parameters affect the residual function and can be used to demonstrate manual structure optimization for simple crystal structures.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Simons, J.M.Roth, G.2015-07-28doi:10.1107/S1600576715012169International Union of CrystallographyUsing a newly created open-source tool Xtal-xplore-R some universal features of the crystallographic residual function have been found, which might help in developing new algorithms suitable for crystal structure solution.enRESIDUAL FUNCTIONS; CRYSTAL STRUCTURE DETERMINATIONThis work presents Xtal-xplore-R, a tool dedicated to the visualization of two-dimensional cuts through the multidimensional crystallographic residual function. It imports arbitrary crystal structures, generates artificial diffraction data, and calculates and investigates the residual function in parameter space. The program serves two major purposes. Firstly, it is part of a more general project dealing with structure determination via global optimization techniques. In this context, the tool is being used to systematically analyse characteristic universal features of the target function (residual function) which can be used to develop appropriate problem-specific heuristic optimization algorithms. Secondly, Xtal-xplore-R is intended as a didactic tool to visualize how changes in atom parameters affect the residual function and can be used to demonstrate manual structure optimization for simple crystal structures.text/htmlXtal-xplore-R: a graphical tool for exploring the residual function involved in crystal structure determinationtext4482015-07-28Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1335med@iucr.org13411600-5767The ash heap of crystallography: restoring forgotten basic knowledgehttp://scripts.iucr.org/cgi-bin/paper?gj5135
A critical analysis of some basic notions often overlooked in crystallographic education is presented to correct some common oversights occurring both in the literature and in textbooks. The crystal forms (face forms), defined in terms of their geometric eigensymmetry, are 47 in number, not 48 as often found in the literature. The split of the dihedron into dome and sphenoid calls for the consideration of the physical properties of the faces building a form; in that case, however, the same criterion should be used for all forms. By taking the handedness of the faces as representative of the physical properties of the faces, the occurrence of 128 crystallographic face forms (97 affine face forms and 31 enantiomorphic pairs) is demonstrated. Next, the correct use of non-coprime Miller indices when a centred unit cell is adopted is shown, and the inconsistent multiplication of Miller indices in the Bravais–Friedel–Donnay–Harker law is pointed out. A geometric derivation of the reflection conditions is reviewed. Finally, the inconsistent presentation of metric restrictions imposed by the structural symmetry is pointed out and corrected.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Nespolo, M.2015-07-18doi:10.1107/S1600576715011206International Union of CrystallographyA critical revision of fundamental crystallographic concepts and the pedagogical approaches used to introduce them is presented.enCRYSTAL FORMS; SYSTEMATIC ABSENCES; MILLER INDICES; SYMMETRY RESTRICTIONS; CRYSTALLOGRAPHIC EDUCATIONA critical analysis of some basic notions often overlooked in crystallographic education is presented to correct some common oversights occurring both in the literature and in textbooks. The crystal forms (face forms), defined in terms of their geometric eigensymmetry, are 47 in number, not 48 as often found in the literature. The split of the dihedron into dome and sphenoid calls for the consideration of the physical properties of the faces building a form; in that case, however, the same criterion should be used for all forms. By taking the handedness of the faces as representative of the physical properties of the faces, the occurrence of 128 crystallographic face forms (97 affine face forms and 31 enantiomorphic pairs) is demonstrated. Next, the correct use of non-coprime Miller indices when a centred unit cell is adopted is shown, and the inconsistent multiplication of Miller indices in the Bravais–Friedel–Donnay–Harker law is pointed out. A geometric derivation of the reflection conditions is reviewed. Finally, the inconsistent presentation of metric restrictions imposed by the structural symmetry is pointed out and corrected.text/htmlThe ash heap of crystallography: restoring forgotten basic knowledgetext4482015-07-18Journal of Applied CrystallographyCopyright (c) 2015 International Union of Crystallography1600-5767teaching and education1290med@iucr.org12981600-5767Computation of diffuse scattering arising from one-phonon excitations in a neutron time-of-flight single-crystal Laue diffraction experimenthttp://scripts.iucr.org/cgi-bin/paper?ks5457
Direct phonon excitation in a neutron time-of-flight single-crystal Laue diffraction experiment has been observed in a single crystal of NaCl. At room temperature both phonon emission and excitation leave characteristic features in the diffuse scattering and these are well reproduced using ab initio phonons from density functional theory (DFT). A measurement at 20 K illustrates the effect of thermal population of the phonons, leaving the features corresponding to phonon excitation and strongly suppressing the phonon annihilation. A recipe is given to compute these effects combining DFT results with the geometry of the neutron experiment.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Gutmann, M.J.Graziano, G.Mukhopadhyay, S.Refson, K.von Zimmermann, M.2015-07-08doi:10.1107/S1600576715010912International Union of CrystallographyA methodology is presented to compute diffuse scattering arising from one-phonon excitations in a time-of-flight neutron single-crystal Laue diffraction experiment from density functional theory results. This methodology is illustrated using NaCl as an example.enNEUTRON TIME-OF-FLIGHT; LAUE DIFFRACTION; SINGLE CRYSTALS; PHONON EXCITATIONDirect phonon excitation in a neutron time-of-flight single-crystal Laue diffraction experiment has been observed in a single crystal of NaCl. At room temperature both phonon emission and excitation leave characteristic features in the diffuse scattering and these are well reproduced using ab initio phonons from density functional theory (DFT). A measurement at 20 K illustrates the effect of thermal population of the phonons, leaving the features corresponding to phonon excitation and strongly suppressing the phonon annihilation. A recipe is given to compute these effects combining DFT results with the geometry of the neutron experiment.text/htmlComputation of diffuse scattering arising from one-phonon excitations in a neutron time-of-flight single-crystal Laue diffraction experimenttext4482015-07-08Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1122med@iucr.org11291600-5767Survey of background scattering from materials found in small-angle neutron scatteringhttp://scripts.iucr.org/cgi-bin/paper?ks5470
Measurements and calculations of beam attenuation and background scattering for common materials placed in a neutron beam are presented over the temperature range of 300–700 K. Time-of-flight (TOF) measurements have also been made, to determine the fraction of the background that is either inelastic or quasi-elastic scattering as measured with a 3He detector. Other background sources considered include double Bragg diffraction from windows or samples, scattering from gases, and phonon scattering from solids. Background from the residual air in detector vacuum vessels and scattering from the 3He detector dome are presented. The thickness dependence of the multiple scattering correction for forward scattering from water is calculated. Inelastic phonon background scattering at small angles for crystalline solids is both modeled and compared with measurements. Methods of maximizing the signal-to-noise ratio by material selection, choice of sample thickness and wavelength, removal of inelastic background by TOF or Be filters, and removal of spin-flip scattering with polarized beam analysis are discussed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Barker, J.G.Mildner, D.F.R.2015-06-27doi:10.1107/S1600576715010729International Union of CrystallographyThe paper describes quantitative methods for determining the background scattering from materials, including gases, liquids and solids, found in small-angle neutron scattering measurements. By understanding the dependence of the background on material type, thickness, wavelength and temperature, the investigator can design experiments that minimize the background scattering and thus improve the statistical accuracy of the background-corrected data.enSMALL-ANGLE NEUTRON SCATTERING; BACKGROUND SCATTERING; MULTIPLE SCATTERING; PHONON SCATTERING; TIME-OF-FLIGHT MEASUREMENTSMeasurements and calculations of beam attenuation and background scattering for common materials placed in a neutron beam are presented over the temperature range of 300–700 K. Time-of-flight (TOF) measurements have also been made, to determine the fraction of the background that is either inelastic or quasi-elastic scattering as measured with a 3He detector. Other background sources considered include double Bragg diffraction from windows or samples, scattering from gases, and phonon scattering from solids. Background from the residual air in detector vacuum vessels and scattering from the 3He detector dome are presented. The thickness dependence of the multiple scattering correction for forward scattering from water is calculated. Inelastic phonon background scattering at small angles for crystalline solids is both modeled and compared with measurements. Methods of maximizing the signal-to-noise ratio by material selection, choice of sample thickness and wavelength, removal of inelastic background by TOF or Be filters, and removal of spin-flip scattering with polarized beam analysis are discussed.text/htmlSurvey of background scattering from materials found in small-angle neutron scatteringtext4482015-06-27Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1055med@iucr.org10711600-5767The experience of the Voyage dans le cristal travelling museum exhibitionhttp://scripts.iucr.org/cgi-bin/paper?kk5194
Crystallography is little known to the public, even though it underpins much of the research into matter in physics, chemistry, new materials and life sciences. On the one hand, crystallography is present in almost every field of scientific or technical activity and also in innovative applications. On the other hand, the origins of crystallography started with humanity's interrogation and interaction with crystals in prehistoric times, which has continued to the present day. These two `views' can be used to focus public interest on crystallography and show children and students the importance of the scientific approach. As an example, this article describes the travelling exhibition Journey into the crystal, which presents to the general public the science and the beauty of matter in the crystalline state. This exhibition takes visitors on a journey of discovery about matter, but also on a journey through time to the beginnings of crystallography.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Hodeau, J.-L.Guinebretiere, R.2015-07-08doi:10.1107/S160057671501064XInternational Union of CrystallographyCrystallography is little known to the public, even though it underpins much of the research into matter in physics, chemistry, new materials and life sciences. This article describes the travelling exhibition Journey into the crystal, which presents to the general public the science and the beauty of matter in the crystalline state with a flavour of crystallography.enDISSEMINATION OF SCIENCE; OUTREACH; CRYSTALLOGRAPHY; EXHIBITIONS; EDUCATIONCrystallography is little known to the public, even though it underpins much of the research into matter in physics, chemistry, new materials and life sciences. On the one hand, crystallography is present in almost every field of scientific or technical activity and also in innovative applications. On the other hand, the origins of crystallography started with humanity's interrogation and interaction with crystals in prehistoric times, which has continued to the present day. These two `views' can be used to focus public interest on crystallography and show children and students the importance of the scientific approach. As an example, this article describes the travelling exhibition Journey into the crystal, which presents to the general public the science and the beauty of matter in the crystalline state. This exhibition takes visitors on a journey of discovery about matter, but also on a journey through time to the beginnings of crystallography.text/htmlThe experience of the Voyage dans le cristal travelling museum exhibitiontext4482015-07-08Journal of Applied CrystallographyCopyright (c) 2015 International Union of Crystallography1600-5767teaching and education1276med@iucr.org12891600-5767Programming new geometry restraints: parallelity of atomic groupshttp://scripts.iucr.org/cgi-bin/paper?vg5020
Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox (cctbx) are presented.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Sobolev, O.V.Afonine, P.V.Adams, P.D.Urzhumtsev, A.2015-07-08doi:10.1107/S1600576715010432International Union of CrystallographyDetails are described of the calculation of new parallelity restraints recently introduced in cctbx and PHENIX.enRESTRAINTS; ATOMIC MODEL REFINEMENT; PARALLEL PLANES; CCTBX; PHENIX; GRADIENT CALCULATIONImprovements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox (cctbx) are presented.text/htmlProgramming new geometry restraints: parallelity of atomic groupstext4482015-07-08Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1130med@iucr.org11411600-5767TEMPy: a Python library for assessment of three-dimensional electron microscopy density fitshttp://scripts.iucr.org/cgi-bin/paper?vg5014
Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Farabella, I.Vasishtan, D.Joseph, A.P.Pandurangan, A.P.Sahota, H.Topf, M.2015-06-27doi:10.1107/S1600576715010092International Union of CrystallographyTEMPy is an object-oriented Python library that provides the means to validate density fits in electron microscopy reconstructions. This article highlights several features of particular interest for this purpose and includes some customized examples.enTHREE-DIMENSIONAL ELECTRON MICROSCOPY; MACROMOLECULAR STRUCTURES; MODEL ASSESSMENTThree-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.text/htmlTEMPy: a Python library for assessment of three-dimensional electron microscopy density fitstext4482015-06-27Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1314med@iucr.org13231600-5767Quantitative evaluation of microtwins and antiphase defects in GaP/Si nanolayers for a III–V photonics platform on silicon using a laboratory X-ray diffraction setupThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?zr5003
This study is carried out in the context of III–V semiconductor monolithic integration on silicon for optoelectronic device applications. X-ray diffraction is combined with atomic force microscopy and scanning transmission electron microscopy for structural characterization of GaP nanolayers grown on Si. GaP has been chosen as the interfacial layer, owing to its low lattice mismatch with Si. But, microtwins and antiphase boundaries are still difficult to avoid in this system. Absolute quantification of the microtwin volume fraction is used for optimization of the growth procedure in order to eliminate these defects. Lateral correlation lengths associated with mean antiphase boundary distances are then evaluated. Finally, optimized growth conditions lead to the annihilation of antiphase domains within the first 10 nm.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ping Wang, Y.Letoublon, A.Nguyen Thanh, T.Bahri, M.Largeau, L.Patriarche, G.Cornet, C.Bertru, N.Le Corre, A.Durand, O.2015-05-31doi:10.1107/S1600576715009954International Union of CrystallographyA laboratory X-ray diffraction setup is reported, which allows quantitative characterization of the microtwin and antiphase domain densities in epitaxial GaP/Si thin layers.enMICROTWINS; ANTIPHASE DEFECTS; GAP/SI NANOLAYERS; SEMICONDUCTORS; LABORATORY X-RAY DIFFRACTIONThis study is carried out in the context of III–V semiconductor monolithic integration on silicon for optoelectronic device applications. X-ray diffraction is combined with atomic force microscopy and scanning transmission electron microscopy for structural characterization of GaP nanolayers grown on Si. GaP has been chosen as the interfacial layer, owing to its low lattice mismatch with Si. But, microtwins and antiphase boundaries are still difficult to avoid in this system. Absolute quantification of the microtwin volume fraction is used for optimization of the growth procedure in order to eliminate these defects. Lateral correlation lengths associated with mean antiphase boundary distances are then evaluated. Finally, optimized growth conditions lead to the annihilation of antiphase domains within the first 10 nm.text/htmlQuantitative evaluation of microtwins and antiphase defects in GaP/Si nanolayers for a III–V photonics platform on silicon using a laboratory X-ray diffraction setupThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-05-31702research papers1600-5767med@iucr.org7101600-5767The `quasi-mosaic' effect in crystals and its applications in modern physicshttp://scripts.iucr.org/cgi-bin/paper?ks5467
`Quasi-mosaicity' is an effect of anisotropy in crystals that permits one to obtain a curvature of internal crystallographic planes that would be flat otherwise. The term `quasi-mosaicity' was introduced by O. Sumbaev in 1957. The concept of `quasi-mosaicity' was then retrieved about ten years ago and was applied to steering of charged-particle beams at the Super Proton Synchrotron at CERN. Beams were deviated by exploiting channeling and volume reflection phenomena in curved crystals that show the `quasi-mosaic' effect. More recently, a crystal of this kind was installed in the Large Hadron Collider at CERN for beam collimation by the UA9 collaboration. Since 2011, another important application involving the `quasi-mosaic' effect has been the focalization of hard X-rays and soft γ-rays. In particular, the possibility of obtaining both high diffraction efficiency and the focalization of a diffracted beam has been proved, which cannot be obtained using traditional diffracting crystals. A comprehensive survey of the physical properties of `quasi-mosaicity' is reported here. Finally, experimental demonstrations for adjustable values of the `quasi-mosaic' curvature are provided.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Camattari, R.Guidi, V.Bellucci, V.Mazzolari, A.2015-06-16doi:10.1107/S1600576715009875International Union of Crystallography`Quasi-mosaicity' is an effect of anisotropy in crystals, which permits one to obtain two curvatures in two perpendicular crystallographic planes. A comprehensive survey of the physical properties and the applications of `quasi-mosaicity' are extensively reported.enQUASI-MOSAICITY; HARD X-RAY FOCALIZATION; CHARGED-PARTICLE BEAM STEERING`Quasi-mosaicity' is an effect of anisotropy in crystals that permits one to obtain a curvature of internal crystallographic planes that would be flat otherwise. The term `quasi-mosaicity' was introduced by O. Sumbaev in 1957. The concept of `quasi-mosaicity' was then retrieved about ten years ago and was applied to steering of charged-particle beams at the Super Proton Synchrotron at CERN. Beams were deviated by exploiting channeling and volume reflection phenomena in curved crystals that show the `quasi-mosaic' effect. More recently, a crystal of this kind was installed in the Large Hadron Collider at CERN for beam collimation by the UA9 collaboration. Since 2011, another important application involving the `quasi-mosaic' effect has been the focalization of hard X-rays and soft γ-rays. In particular, the possibility of obtaining both high diffraction efficiency and the focalization of a diffracted beam has been proved, which cannot be obtained using traditional diffracting crystals. A comprehensive survey of the physical properties of `quasi-mosaicity' is reported here. Finally, experimental demonstrations for adjustable values of the `quasi-mosaic' curvature are provided.text/htmlThe `quasi-mosaic' effect in crystals and its applications in modern physicstext4482015-06-16Journal of Applied CrystallographyCopyright (c) 2015 International Union of Crystallography1600-5767feature articlesmed@iucr.org1600-5767BINoculars: data reduction and analysis software for two-dimensional detectors in surface X-ray diffractionhttp://scripts.iucr.org/cgi-bin/paper?rg5089
BINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques. This paper covers the design and the underlying methods employed in this software package and explains how BINoculars can be used to improve the workflow of surface X-ray diffraction measurements and analysis.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Roobol, S.Onderwaater, W.Drnec, J.Felici, R.Frenken, J.2015-06-27doi:10.1107/S1600576715009607International Union of CrystallographyBINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector.enDATA ANALYSIS; DATA REDUCTION; RECIPROCAL-SPACE MAPPING; X-RAY DIFFRACTIONBINoculars is a tool for data reduction and analysis of large sets of surface diffraction data that have been acquired with a two-dimensional X-ray detector. The intensity of each pixel of a two-dimensional detector is projected onto a three-dimensional grid in reciprocal-lattice coordinates using a binning algorithm. This allows for fast acquisition and processing of high-resolution data sets and results in a significant reduction of the size of the data set. The subsequent analysis then proceeds in reciprocal space. It has evolved from the specific needs of the ID03 beamline at the ESRF, but it has a modular design and can be easily adjusted and extended to work with data from other beamlines or from other measurement techniques. This paper covers the design and the underlying methods employed in this software package and explains how BINoculars can be used to improve the workflow of surface X-ray diffraction measurements and analysis.text/htmlBINoculars: data reduction and analysis software for two-dimensional detectors in surface X-ray diffractiontext4482015-06-27Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1324med@iucr.org13291600-5767A laboratory-based Laue X-ray diffraction system for enhanced imaging range and surface grain mappinghttp://scripts.iucr.org/cgi-bin/paper?pd5057
Although CCD X-ray detectors can be faster to use, their large-area versions can be much more expensive than similarly sized photographic plate detectors. When indexing X-ray diffraction patterns, large-area detectors can prove very advantageous as they provide more spots, which makes fitting an orientation easier. On the other hand, when looking for single crystals in a polycrystalline sample, the speed of CCD detectors is more useful. A new setup is described here which overcomes some of the limitations of limited-range CCD detectors to make them more useful for indexing, whilst at the same time making it much quicker to find single crystals within a larger polycrystalline structure. This was done by combining a CCD detector with a six-axis goniometer, allowing the compilation of images from different angles into a wide-angled image. Automated scans along the sample were coupled with image processing techniques to produce grain maps, which can then be used to provide a strategy to extract single crystals from a polycrystal.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Whitley, W.Stock, C.Huxley, A.D.2015-06-27doi:10.1107/S1600576715009097International Union of CrystallographyApparatus is described for the purpose of automated grain mapping of polycrystalline samples within a laboratory environment, using a motorized sample stage and a CCD detector. The limitations that come from using a faster detector of relatively small surface are countered using an automated translation stage.enLABORATORY-BASED LAUE X-RAY DIFFRACTION; GRAIN MAPPINGAlthough CCD X-ray detectors can be faster to use, their large-area versions can be much more expensive than similarly sized photographic plate detectors. When indexing X-ray diffraction patterns, large-area detectors can prove very advantageous as they provide more spots, which makes fitting an orientation easier. On the other hand, when looking for single crystals in a polycrystalline sample, the speed of CCD detectors is more useful. A new setup is described here which overcomes some of the limitations of limited-range CCD detectors to make them more useful for indexing, whilst at the same time making it much quicker to find single crystals within a larger polycrystalline structure. This was done by combining a CCD detector with a six-axis goniometer, allowing the compilation of images from different angles into a wide-angled image. Automated scans along the sample were coupled with image processing techniques to produce grain maps, which can then be used to provide a strategy to extract single crystals from a polycrystal.text/htmlA laboratory-based Laue X-ray diffraction system for enhanced imaging range and surface grain mappingtext4482015-06-27Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767laboratory notes1342med@iucr.org13451600-5767XTOP: high-resolution X-ray diffraction and imaginghttp://scripts.iucr.org/cgi-bin/paper?me0579
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Favre-Nicolin, V.Baruchel, J.Renevier, H.Eymery, J.Borbély, A.2015-05-31doi:10.1107/S160057671500895XInternational Union of CrystallographyThe latest virtual special issue of Journal of Applied Crystallography includes some highlights of the 12th Conference on High-Resolution X-ray Diffraction and Imaging (XTOP), which took place in Villard-de-Lans and Grenoble in September 2014.enHIGH-RESOLUTION X-RAY DIFFRACTION; IMAGING; EDITORIALtext/htmlXTOP: high-resolution X-ray diffraction and imagingtext483Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-05-31620editorial1600-5767med@iucr.org6201600-5767Magnetite nanoparticles for nonradionuclide brachytherapyThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?fv5027
Magnetite nanoparticles possess several properties that can make them useful for targeted delivery of radiation to tumors for the purpose of brachytherapy. Such particles are biodegradable and magnetic and can emit secondary radiation when irradiated by an external source. In this work, the dose distribution around a magnetite particle of 10 nm diameter being irradiated by monochromatic X-rays with energies in the range 4–60 keV is calculated.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Safronov, V.Sozontov, E.Polikarpov, M.2015-05-22doi:10.1107/S1600576715008900International Union of CrystallographyMonte Carlo simulation of the dose distribution in water around magnetite nanoparticles irradiated by monochromatic X-rays is presented.enMAGNETITE; NANOPARTICLES; BRACHYTHERAPYMagnetite nanoparticles possess several properties that can make them useful for targeted delivery of radiation to tumors for the purpose of brachytherapy. Such particles are biodegradable and magnetic and can emit secondary radiation when irradiated by an external source. In this work, the dose distribution around a magnetite particle of 10 nm diameter being irradiated by monochromatic X-rays with energies in the range 4–60 keV is calculated.text/htmlMagnetite nanoparticles for nonradionuclide brachytherapyThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-05-22690research papers1600-5767med@iucr.org6921600-5767CRISTALES: a world to discover. An exhibition for schools and universitieshttp://scripts.iucr.org/cgi-bin/paper?kk5195
The exhibition CRISTALES: a world to discover is a teaching/outreach activity whose main goals are to increase awareness of the importance of crystallography and its role in everyday life in modern society, motivate young people, and promote education and research in crystallography. CRISTALES is designed to inspire the audience with a careful design and a view of crystallography that places the emphasis not only on the most important contributions of crystallography to society's welfare, including new materials and biomedical research, but also on those aspects of crystallography related to art and the mind. This article describes the simplest version of the exhibition, composed of 14 posters that have been created specifically for schools and universities. Each poster displays an image that is both aesthetically powerful and scientifically intriguing, so as to provoke the curiosity of the students. The posters also contain a brief text explaining the image and its relation to crystallography and a QR code that links the poster to a web page containing further information.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Garcia-Ruiz, J.M.Otalora, F.Garcia-Caballero, A.González-Ramírez, L.A.Verdugo-Escamilla, C.2015-06-16doi:10.1107/S1600576715007724International Union of CrystallographyCRISTALES: a world to discover is a teaching/outreach exhibition for schools and universities, offering a groundbreaking view of crystallography and its main contributions to society.enCRYSTALLIZATION; CRYSTALLOGRAPHY; EXHIBITIONS; EDUCATION; OUTREACHThe exhibition CRISTALES: a world to discover is a teaching/outreach activity whose main goals are to increase awareness of the importance of crystallography and its role in everyday life in modern society, motivate young people, and promote education and research in crystallography. CRISTALES is designed to inspire the audience with a careful design and a view of crystallography that places the emphasis not only on the most important contributions of crystallography to society's welfare, including new materials and biomedical research, but also on those aspects of crystallography related to art and the mind. This article describes the simplest version of the exhibition, composed of 14 posters that have been created specifically for schools and universities. Each poster displays an image that is both aesthetically powerful and scientifically intriguing, so as to provoke the curiosity of the students. The posters also contain a brief text explaining the image and its relation to crystallography and a QR code that links the poster to a web page containing further information.text/htmlCRISTALES: a world to discover. An exhibition for schools and universitiestext4482015-06-16Journal of Applied CrystallographyCopyright (c) 2015 International Union of Crystallography1600-5767teaching and educationmed@iucr.org1600-5767McSAS: software for the retrieval of model parameter distributions from scattering patternshttp://scripts.iucr.org/cgi-bin/paper?vg5017
A user-friendly open-source Monte Carlo regression package (McSAS) is presented, which structures the analysis of small-angle scattering (SAS) using uncorrelated shape-similar particles (or scattering contributions). The underdetermined problem is solvable, provided that sufficient external information is available. Based on this, the user picks a scatterer contribution model (or `shape') from a comprehensive library and defines variation intervals of its model parameters. A multitude of scattering contribution models are included, including prolate and oblate nanoparticles, core–shell objects, several polymer models, and a model for densely packed spheres. Most importantly, the form-free Monte Carlo nature of McSAS means it is not necessary to provide further restrictions on the mathematical form of the parameter distribution; without prior knowledge, McSAS is able to extract complex multimodal or odd-shaped parameter distributions from SAS data. When provided with data on an absolute scale with reasonable uncertainty estimates, the software outputs model parameter distributions in absolute volume fraction, and provides the modes of the distribution (e.g. mean, variance etc.). In addition to facilitating the evaluation of (series of) SAS curves, McSAS also helps in assessing the significance of the results through the addition of uncertainty estimates to the result. The McSAS software can be integrated as part of an automated reduction and analysis procedure in laboratory instruments or at synchrotron beamlines.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Bressler, I.Pauw, B.R.Thünemann, A.F.2015-05-22doi:10.1107/S1600576715007347International Union of CrystallographyA user-friendly open-source Monte Carlo regression package (McSAS) is presented, which aids in the analysis of scattering patterns from uncorrelated, shape-similar scatterers. The Monte Carlo nature necessitates an assumption on the elementary shape of the scatterer, but can resolve the shape-defining parameter distributions without restrictions on the mathematical form of the distribution.enSMALL-ANGLE SCATTERING; MONTE CARLO; DATA ANALYSIS SOFTWARE; DISPERSE SAMPLESA user-friendly open-source Monte Carlo regression package (McSAS) is presented, which structures the analysis of small-angle scattering (SAS) using uncorrelated shape-similar particles (or scattering contributions). The underdetermined problem is solvable, provided that sufficient external information is available. Based on this, the user picks a scatterer contribution model (or `shape') from a comprehensive library and defines variation intervals of its model parameters. A multitude of scattering contribution models are included, including prolate and oblate nanoparticles, core–shell objects, several polymer models, and a model for densely packed spheres. Most importantly, the form-free Monte Carlo nature of McSAS means it is not necessary to provide further restrictions on the mathematical form of the parameter distribution; without prior knowledge, McSAS is able to extract complex multimodal or odd-shaped parameter distributions from SAS data. When provided with data on an absolute scale with reasonable uncertainty estimates, the software outputs model parameter distributions in absolute volume fraction, and provides the modes of the distribution (e.g. mean, variance etc.). In addition to facilitating the evaluation of (series of) SAS curves, McSAS also helps in assessing the significance of the results through the addition of uncertainty estimates to the result. The McSAS software can be integrated as part of an automated reduction and analysis procedure in laboratory instruments or at synchrotron beamlines.text/htmlMcSAS: software for the retrieval of model parameter distributions from scattering patternstext483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-05-22962computer programs1600-5767med@iucr.org9691600-5767Why crystal structure analysis works: a one-dimensional crystallography teaching toolhttp://scripts.iucr.org/cgi-bin/paper?gj5136
A teaching tool is proposed to help beginner students of crystallography understand how crystallographic calculations work. Examples of the most important methods taught in X-ray crystallography courses have been adapted to a one-dimensional hypothetical structure. All calculations can be carried out in class with a scientific calculator or by using a simple spreadsheet.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Pinkerton, A.A.2015-05-22doi:10.1107/S1600576715007116International Union of CrystallographyA teaching tool for X-ray crystallography using a one dimensional approach is presented.enX-RAY CRYSTALLOGRAPHY; TEACHING TOOLS; ONE-DIMENSIONAL CALCULATIONSA teaching tool is proposed to help beginner students of crystallography understand how crystallographic calculations work. Examples of the most important methods taught in X-ray crystallography courses have been adapted to a one-dimensional hypothetical structure. All calculations can be carried out in class with a scientific calculator or by using a simple spreadsheet.text/htmlWhy crystal structure analysis works: a one-dimensional crystallography teaching tooltext483Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-05-22901teaching and education1600-5767med@iucr.org9051600-5767SCT: a suite of programs for comparing atomistic models with small-angle scattering datahttp://scripts.iucr.org/cgi-bin/paper?po5031
Small-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Wright, D.W.Perkins, S.J.2015-05-09doi:10.1107/S1600576715007062International Union of CrystallographyThe SCT suite of tools for the atomistic modelling of X-ray and neutron scattering curves has resulted in 77 macromolecular structures to date. SCT is now made publicly available as open source, alongside an easier-to-use reimplementation of the same algorithms in Python.enANALYTICAL ULTRACENTRIFUGATION; CONSTRAINED MODELLING; HYDRATION SHELLS; NEUTRON SCATTERING; X-RAY SCATTERINGSmall-angle X-ray and neutron scattering techniques characterize proteins in solution and complement high-resolution structural studies. They are of particular utility when large proteins cannot be crystallized or when the structure is altered by solution conditions. Atomistic models of the averaged structure can be generated through constrained modelling, a technique in which known domain or subunit structures are combined with linker models to produce candidate global conformations. By randomizing the configuration adopted by the different elements of the model, thousands of candidate structures are produced. Next, theoretical scattering curves are generated for each model for trial-and-error fits to the experimental data. From these, a small family of best-fit models is identified. In order to facilitate both the computation of theoretical scattering curves from atomistic models and their comparison with experiment, the SCT suite of tools was developed. SCT also includes programs that provide sequence-based estimates of protein volume (either incorporating hydration or not) and add a hydration layer to models for X-ray scattering modelling. The original SCT software, written in Fortran, resulted in the first atomistic scattering structures to be deposited in the Protein Data Bank, and 77 structures for antibodies, complement proteins and anionic oligosaccharides were determined between 1998 and 2014. For the first time, this software is publicly available, alongside an easier-to-use reimplementation of the same algorithms in Python. Both versions of SCT have been released as open-source software under the Apache 2 license and are available for download from https://github.com/dww100/sct.text/htmlSCT: a suite of programs for comparing atomistic models with small-angle scattering datatext483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-05-09953computer programs1600-5767med@iucr.org9611600-5767Ab initio simulation of diffractometer instrumental function for high-resolution X-ray diffractionThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?fv5029
Modeling of the X-ray diffractometer instrumental function for a given optics configuration is important both for planning experiments and for the analysis of measured data. A fast and universal method for instrumental function simulation, suitable for fully automated computer realization and describing both coplanar and noncoplanar measurement geometries for any combination of X-ray optical elements, is proposed. The method can be identified as semi-analytical backward ray tracing and is based on the calculation of a detected signal as an integral of X-ray intensities for all the rays reaching the detector. The high speed of calculation is provided by the expressions for analytical integration over the spatial coordinates that describe the detection point. Consideration of the three-dimensional propagation of rays without restriction to the diffraction plane provides the applicability of the method for noncoplanar geometry and the accuracy for characterization of the signal from a two-dimensional detector. The correctness of the simulation algorithm is checked in the following two ways: by verifying the consistency of the calculated data with the patterns expected for certain simple limiting cases and by comparing measured reciprocal-space maps with the corresponding maps simulated by the proposed method for the same diffractometer configurations. Both kinds of tests demonstrate the agreement of the simulated instrumental function shape with the measured data.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Mikhalychev, A.Benediktovitch, A.Ulyanenkova, T.Ulyanenkov, A.2015-05-09doi:10.1107/S1600576715006986International Union of CrystallographyA method for the simulation of the diffractometer instrumental function for high-resolution X-ray diffraction, applicable for coplanar and noncoplanar measurement geometry and for any combination of X-ray optical elements, is proposed. Good agreement is demonstrated between the measured and the simulated reciprocal-space maps, which account for the instrumental function.enDIFFRACTOMETER INSTRUMENTAL FUNCTION; HIGH-RESOLUTION X-RAY DIFFRACTION; AB INITIO SIMULATIONModeling of the X-ray diffractometer instrumental function for a given optics configuration is important both for planning experiments and for the analysis of measured data. A fast and universal method for instrumental function simulation, suitable for fully automated computer realization and describing both coplanar and noncoplanar measurement geometries for any combination of X-ray optical elements, is proposed. The method can be identified as semi-analytical backward ray tracing and is based on the calculation of a detected signal as an integral of X-ray intensities for all the rays reaching the detector. The high speed of calculation is provided by the expressions for analytical integration over the spatial coordinates that describe the detection point. Consideration of the three-dimensional propagation of rays without restriction to the diffraction plane provides the applicability of the method for noncoplanar geometry and the accuracy for characterization of the signal from a two-dimensional detector. The correctness of the simulation algorithm is checked in the following two ways: by verifying the consistency of the calculated data with the patterns expected for certain simple limiting cases and by comparing measured reciprocal-space maps with the corresponding maps simulated by the proposed method for the same diffractometer configurations. Both kinds of tests demonstrate the agreement of the simulated instrumental function shape with the measured data.text/htmlAb initio simulation of diffractometer instrumental function for high-resolution X-ray diffractionThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-05-09679research papers1600-5767med@iucr.org6891600-5767Surface-treated self-standing curved crystals as high-efficiency elements for X- and γ-ray optics: theory and experimentThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?ze5003
The efficiency of a Laue lens for X- and γ-ray focusing in the energy range 60–600 keV is closely linked to the diffraction efficiency of the single crystals composing the lens. A powerful focusing system is crucial for applications like medical imaging and X-ray astronomy where wide beams must be focused. Mosaic crystals with a high density, such as Cu or Au, and bent crystals with curved diffracting planes (CDPs) are considered for the realization of a focusing system for γ-rays, owing to their high diffraction efficiency in a predetermined angular range. In this work, a comparison of the efficiency of CDP crystals and Cu and Au mosaic crystals was performed on the basis of the theory of X-ray diffraction. Si, GaAs and Ge CDP crystals with optimized thicknesses and moderate radii of curvature of several tens of metres demonstrate comparable or superior performance with respect to the higher atomic number mosaic crystals generally used. In order to increase the efficiency of the lens further, a stack of several CDP crystals is proposed as an optical element. CDP crystals were obtained by a surface-damage method, and a stack of two surface-damaged bent Si crystals was prepared and tested. Rocking curves of the stack were performed with synchrotron radiation at 19 keV to check the lattice alignment: they exhibited only one diffraction peak.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Bonnini, E.Buffagni, E.Zappettini, A.Doyle, S.Ferrari, C.2015-04-25doi:10.1107/S1600576715006809International Union of CrystallographyIt is demonstrated that crystals with curved diffracting planes made of relatively light elements, such as silicon, germanium and gallium arsenide, in the Laue diffraction geometry and in an energy range between 60 and 600 keV can reach a higher diffraction efficiency than more dense mosaic crystals such as copper, silver and gold. In particular, self-standing curved crystals can be used as elements in γ-ray lenses.enX-RAY FOCUSING LENSES; INTEGRATED REFLECTIVITY; CURVED CRYSTALS; CRYSTAL STACKSThe efficiency of a Laue lens for X- and γ-ray focusing in the energy range 60–600 keV is closely linked to the diffraction efficiency of the single crystals composing the lens. A powerful focusing system is crucial for applications like medical imaging and X-ray astronomy where wide beams must be focused. Mosaic crystals with a high density, such as Cu or Au, and bent crystals with curved diffracting planes (CDPs) are considered for the realization of a focusing system for γ-rays, owing to their high diffraction efficiency in a predetermined angular range. In this work, a comparison of the efficiency of CDP crystals and Cu and Au mosaic crystals was performed on the basis of the theory of X-ray diffraction. Si, GaAs and Ge CDP crystals with optimized thicknesses and moderate radii of curvature of several tens of metres demonstrate comparable or superior performance with respect to the higher atomic number mosaic crystals generally used. In order to increase the efficiency of the lens further, a stack of several CDP crystals is proposed as an optical element. CDP crystals were obtained by a surface-damage method, and a stack of two surface-damaged bent Si crystals was prepared and tested. Rocking curves of the stack were performed with synchrotron radiation at 19 keV to check the lattice alignment: they exhibited only one diffraction peak.text/htmlSurface-treated self-standing curved crystals as high-efficiency elements for X- and γ-ray optics: theory and experimentThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-25666research papers1600-5767med@iucr.org6711600-5767Inception and movement of a `subgrain boundary precursor' in ice under an applied stress, observed by X-ray synchrotron radiation Bragg imagingThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?nb5140
Basal slip of dislocations, the easiest deformation mechanism of ice crystals, does not allow a response to any strain state. The first steps of another mechanism, with a moving subgrain boundary precursor region, which permits accommodating the effect of an applied load, is investigated on an ice single crystal, mainly using synchrotron radiation Bragg diffraction imaging. During this process, the evolution of the local integrated intensity shows that there is both a general multiplication of dislocations within the crystal and a movement of basal dislocations towards the surface. The `subgrain boundary precursor' region evolves towards a classical grain boundary when further deformed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Philip, A.Capolo, L.Meyssonnier, J.Baruchel, J.2015-04-25doi:10.1107/S1600576715006342International Union of CrystallographyBoth optical microscopy with polarized light and polychromatic beam synchrotron X-ray diffraction imaging (white-beam topography) are used to study in situ the way an ice single-crystal deforms.enICE; SINGLE-CRYSTAL BRAGG DIFFRACTION; DISLOCATIONS; DEFORMATION MECHANISMBasal slip of dislocations, the easiest deformation mechanism of ice crystals, does not allow a response to any strain state. The first steps of another mechanism, with a moving subgrain boundary precursor region, which permits accommodating the effect of an applied load, is investigated on an ice single crystal, mainly using synchrotron radiation Bragg diffraction imaging. During this process, the evolution of the local integrated intensity shows that there is both a general multiplication of dislocations within the crystal and a movement of basal dislocations towards the surface. The `subgrain boundary precursor' region evolves towards a classical grain boundary when further deformed.text/htmlInception and movement of a `subgrain boundary precursor' in ice under an applied stress, observed by X-ray synchrotron radiation Bragg imagingThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-25672research papers1600-5767med@iucr.org6781600-5767Lip Lin Koh (1935–2015)http://scripts.iucr.org/cgi-bin/paper?es0411
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Vittal, J.J.2015-04-16doi:10.1107/S1600576715006500International Union of CrystallographyObituary for Lip Lin Koh.enOBITUARYtext/htmlLip Lin Koh (1935–2015)text483Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-04-16976crystallographers1600-5767med@iucr.org9761600-5767A step towards long-wavelength protein crystallography: subjecting protein crystals to a vacuumhttp://scripts.iucr.org/cgi-bin/paper?yr5002
Using the UHV experimental endstation on the soft X-ray beamline at the Australian Synchrotron, lysozyme and proteinase K crystals have been exposed to a vacuum of 10−5 mbar, prior to flash-cooling in a bath of liquid nitrogen. Subsequent data collection on the MX2 beamline at the Australian Synchrotron demonstrated that, for lysozyme and proteinase K, it is possible to subject these mounted crystals to a vacuum pressure of 10−5 mbar without destroying the crystal lattice. Despite the lower data quality of the vacuum-pumped crystals compared with control crystals, it is demonstrated that the protein crystals can survive in a vacuum under suitable conditions.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Panjikar, S.Thomsen, L.O'Donnell, K.M.Riboldi-Tunnicliffe, A.2015-05-09doi:10.1107/S1600576715006147International Union of CrystallographyProtein crystals have been subjected to a vacuum pressure of 10−5 mbar prior to flash-cooling, and data acquired at either 7 or 13 keV.enLYSOZYME; PROTEINASE K; VACUUM; LONG-WAVELENGTH CRYSTALLOGRAPHY; SULFUR SINGLE-WAVELENGTH ANOMALOUS DIFFRACTIONUsing the UHV experimental endstation on the soft X-ray beamline at the Australian Synchrotron, lysozyme and proteinase K crystals have been exposed to a vacuum of 10−5 mbar, prior to flash-cooling in a bath of liquid nitrogen. Subsequent data collection on the MX2 beamline at the Australian Synchrotron demonstrated that, for lysozyme and proteinase K, it is possible to subject these mounted crystals to a vacuum pressure of 10−5 mbar without destroying the crystal lattice. Despite the lower data quality of the vacuum-pumped crystals compared with control crystals, it is demonstrated that the protein crystals can survive in a vacuum under suitable conditions.text/htmlA step towards long-wavelength protein crystallography: subjecting protein crystals to a vacuumtext483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-05-09913short communications1600-5767med@iucr.org9161600-5767Monochromatic computed microtomography using laboratory and synchrotron sources and X-ray fluorescence analysis for comprehensive analysis of structural changes in bonesThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?zc5004
A combination of X-ray tomography at different wavelengths and X-ray fluorescence analysis was applied in the study of two types of bone tissue changes: prolonged presence in microgravity conditions and age-related bone growth. The proximal tail vertebrae of geckos were selected for investigation because they do not bear the supporting load in locomotion, which allows them to be considered as an independent indicator of gravitational influence. For the vertebrae of geckos no significant differences were revealed in the elemental composition of the flight samples and the synchronous control samples. In addition, the gecko bone tissue samples from the jaw apparatus, spine and shoulder girdle were measured. The dynamics of structural changes in the bone tissue growth was studied using samples of a human fetal hand. The hands of human fetuses of 11–15 weeks were studied. Autonomous zones of calcium accumulation were found not only in individual fingers but in each of the investigated phalanges. The results obtained are discussed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Buzmakov, A.Chukalina, M.Nikolaev, D.Gulimova, V.Saveliev, S.Tereschenko, E.Seregin, A.Senin, R.Zolotov, D.Prun, V.Shaefer, G.Asadchikov, V.2015-05-31doi:10.1107/S1600576715006214International Union of CrystallographyStructural changes in vertebrate bone tissues caused by bone growth or by weightlessness were studied using a combination of X-ray tomography at different wavelengths and X-ray fluorescence analysis.enMONOCHROMATIC COMPUTED MICROTOMOGRAPHY; X-RAY FLUORESCENCE ANALYSIS; BONEA combination of X-ray tomography at different wavelengths and X-ray fluorescence analysis was applied in the study of two types of bone tissue changes: prolonged presence in microgravity conditions and age-related bone growth. The proximal tail vertebrae of geckos were selected for investigation because they do not bear the supporting load in locomotion, which allows them to be considered as an independent indicator of gravitational influence. For the vertebrae of geckos no significant differences were revealed in the elemental composition of the flight samples and the synchronous control samples. In addition, the gecko bone tissue samples from the jaw apparatus, spine and shoulder girdle were measured. The dynamics of structural changes in the bone tissue growth was studied using samples of a human fetal hand. The hands of human fetuses of 11–15 weeks were studied. Autonomous zones of calcium accumulation were found not only in individual fingers but in each of the investigated phalanges. The results obtained are discussed.text/htmlMonochromatic computed microtomography using laboratory and synchrotron sources and X-ray fluorescence analysis for comprehensive analysis of structural changes in bonesThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text3482015-05-31Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers693med@iucr.org7011600-5767Calculation of scattering patterns from phase-shifting objects using the Radon transform. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?ks9293
The affiliations for the authors of J. Appl. Cryst. (2011), 44, 1157–1163 are corrected.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Treimer, W.Feye-Treimer, U.2015-04-16doi:10.1107/S1600576715006111International Union of CrystallographyThe affiliations for the authors of J. Appl. Cryst. (2011), 44, 1157–1163 are corrected.enSCATTERING METHODS; PHASE-SHIFTING OBJECTS; RADON TRANSFORM; SCATTERING PATTERN CALCULATIONThe affiliations for the authors of J. Appl. Cryst. (2011), 44, 1157–1163 are corrected.text/htmlCalculation of scattering patterns from phase-shifting objects using the Radon transform. Corrigendumtext483Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-04-16975addenda and errata1600-5767med@iucr.org9751600-5767DSR: enhanced modelling and refinement of disordered structures with SHELXLhttp://scripts.iucr.org/cgi-bin/paper?fs5104
One of the remaining challenges in single-crystal structure refinement is the proper description of disorder in crystal structures. This paper describes a computer program that performs semi-automatic modelling of disordered moieties in SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8.]. The new program contains a database that includes molecular fragments and their corresponding stereochemical restraints, and a placement procedure to place these fragments on the desired position in the unit cell. The program is also suitable for speeding up model building of well ordered crystal structures.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Kratzert, D.Holstein, J.J.Krossing, I.2015-04-25doi:10.1107/S1600576715005580International Union of CrystallographyThe new computer program DSR enables semi-automatic modelling of disordered or well ordered moieties in crystal structures via a placement procedure of molecular fragments and corresponding stereochemical restraints from a database.enX-RAY STRUCTURE; REFINEMENT; DISORDER; SHELXL; MOLECULAR FRAGMENTSOne of the remaining challenges in single-crystal structure refinement is the proper description of disorder in crystal structures. This paper describes a computer program that performs semi-automatic modelling of disordered moieties in SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8.]. The new program contains a database that includes molecular fragments and their corresponding stereochemical restraints, and a placement procedure to place these fragments on the desired position in the unit cell. The program is also suitable for speeding up model building of well ordered crystal structures.text/htmlDSR: enhanced modelling and refinement of disordered structures with SHELXLtext483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-25933computer programs1600-5767med@iucr.org9381600-5767Characterization of dislocations in germanium layers grown on (011)- and (111)-oriented silicon by coplanar and noncoplanar X-ray diffractionThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?ze5001
Strained germanium grown on silicon with nonstandard surface orientations like (011) or (111) is a promising material for various semiconductor applications, for example complementary metal-oxide semiconductor transistors. However, because of the large mismatch between the lattice constants of silicon and germanium, the growth of such systems is challenged by nucleation and propagation of threading and misfit dislocations that degrade the electrical properties. To analyze the dislocation microstructure of Ge films on Si(011) and Si(111), a set of reciprocal space maps and profiles measured in noncoplanar geometry was collected. To process the data, the approach proposed by Kaganer, Köhler, Schmidbauer, Opitz & Jenichen [Phys. Rev. B, (1997), 55, 1793–1810] has been generalized to an arbitrary surface orientation, arbitrary dislocation line direction and noncoplanar measurement scheme.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Benediktovitch, A.Zhylik, A.Ulyanenkova, T.Myronov, M.Ulyanenkov, A.2015-04-16doi:10.1107/S1600576715005397International Union of CrystallographyThe generalization of the theoretical approach suggested by Kaganer et al. [Phys. Rev. B, (1997), 55, 1793–1810] to an arbitrary surface orientation, arbitrary dislocation line direction and noncoplanar measurement scheme was developed. It was applied to study the dislocation microstructure of Ge films on Si(011) and Si(111) based on a set of reciprocal space maps and profiles measured in noncoplanar geometry.enSTRAINED GERMANIUM; SILICON; COMPLEMENTARY METAL-OXIDE SEMICONDUCTORS; NONCOPLANAR X-RAY DIFFRACTIONStrained germanium grown on silicon with nonstandard surface orientations like (011) or (111) is a promising material for various semiconductor applications, for example complementary metal-oxide semiconductor transistors. However, because of the large mismatch between the lattice constants of silicon and germanium, the growth of such systems is challenged by nucleation and propagation of threading and misfit dislocations that degrade the electrical properties. To analyze the dislocation microstructure of Ge films on Si(011) and Si(111), a set of reciprocal space maps and profiles measured in noncoplanar geometry was collected. To process the data, the approach proposed by Kaganer, Köhler, Schmidbauer, Opitz & Jenichen [Phys. Rev. B, (1997), 55, 1793–1810] has been generalized to an arbitrary surface orientation, arbitrary dislocation line direction and noncoplanar measurement scheme.text/htmlCharacterization of dislocations in germanium layers grown on (011)- and (111)-oriented silicon by coplanar and noncoplanar X-ray diffractionThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-16655research papers1600-5767med@iucr.org6651600-5767Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical studyThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?nb5138
Crystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and `relaxed' after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Dupraz, M.Beutier, G.Rodney, D.Mordehai, D.Verdier, M.2015-04-16doi:10.1107/S1600576715005324International Union of CrystallographyCrystal defects can be identified by their fingerprint in coherent X-ray diffraction patterns. Realistic defects in face-centred cubic nanocrystals are studied numerically, revealing various signatures in diffraction patterns depending on the Miller indices and providing an identification method.enDISLOCATIONS; STACKING FAULTS; FACE-CENTRED CUBIC NANOCRYSTALS; COHERENT X-RAY DIFFRACTIONCrystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and `relaxed' after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal.text/htmlSignature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical studyThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-16621research papers1600-5767med@iucr.org6441600-5767A look-up table based approach to characterize crystal twinning for synchrotron X-ray Laue microdiffraction scanshttp://scripts.iucr.org/cgi-bin/paper?nb5143
An automated method has been developed to characterize the type and spatial distribution of twinning in crystal orientation maps from synchrotron X-ray Laue microdiffraction results. The method relies on a look-up table approach. Taking into account the twin axis and twin plane for plausible rotation and reflection twins, respectively, and the point group symmetry operations for a specific crystal, a look-up table listing crystal-specific rotation angle–axis pairs, which reveal the orientation relationship between the twin and the parent lattice, is generated. By comparing these theoretical twin–parent orientation relationships in the look-up table with the measured misorientations, twin boundaries are mapped automatically from Laue microdiffraction raster scans with thousands of data points. Taking advantage of the high orientation resolution of the Laue microdiffraction method, this automated approach is also applicable to differentiating twinning elements among multiple twinning modes in any crystal system.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Li, Y.Wan, L.Chen, K.2015-04-25doi:10.1107/S1600576715004896International Union of CrystallographyAn automated method has been developed to characterize the type and spatial distribution of twinning in crystal orientation maps from synchrotron X-ray Laue microdiffraction results.enTWINNING; SYNCHROTRON X-RAY LAUE MICRODIFFRACTION; CRYSTAL ORIENTATION MAPS; LOOK-UP TABLESAn automated method has been developed to characterize the type and spatial distribution of twinning in crystal orientation maps from synchrotron X-ray Laue microdiffraction results. The method relies on a look-up table approach. Taking into account the twin axis and twin plane for plausible rotation and reflection twins, respectively, and the point group symmetry operations for a specific crystal, a look-up table listing crystal-specific rotation angle–axis pairs, which reveal the orientation relationship between the twin and the parent lattice, is generated. By comparing these theoretical twin–parent orientation relationships in the look-up table with the measured misorientations, twin boundaries are mapped automatically from Laue microdiffraction raster scans with thousands of data points. Taking advantage of the high orientation resolution of the Laue microdiffraction method, this automated approach is also applicable to differentiating twinning elements among multiple twinning modes in any crystal system.text/htmlA look-up table based approach to characterize crystal twinning for synchrotron X-ray Laue microdiffraction scanstext483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-25747research papers1600-5767med@iucr.org7571600-5767Characterization of defects in mono-like silicon for photovoltaic applications using X-ray Bragg diffraction imagingThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?nb5142
Rocking curve imaging (projection and section X-ray topography) has been used to study the generation and propagation of defects at the junctions between and above the seed crystals in mono-like silicon ingots. The images of different kinds of defects such as precipitates, dislocations and twins in the integrated intensity, full width at half-maximum and peak position maps resulting from the experiment have been studied. The qualitative and quantitative information that can be extracted from these maps, in particular the contrast of the images of the various defects, is discussed. These defects have a detrimental effect on solar cell efficiency and their detailed investigation allows clues to be obtained in order to improve the growth process. This work shows that synchrotron X-ray diffraction imaging techniques, because of their high angular resolution (<10−4°) and large field of view (several mm2), constitute a powerful tool for investigating the initial stages of growth of directionally solidified mono-like silicon.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Tsoutsouva, M.G.Oliveira, V.A.Baruchel, J.Camel, D.Marie, B.Lafford, T.A.2015-04-16doi:10.1107/S1600576715004926International Union of CrystallographyRocking curve imaging (projection and section X-ray topography) has been used to study different kinds of defects such as precipitates, dislocations and twins in directionally solidified mono-like silicon ingots. The qualitative and quantitative information extracted from the reconstructed integrated intensity, FWHM and peak position maps provides clues about the initial stages of silicon growth.enDEFECT CHARACTERIZATION; PHOTOVOLTAIC APPLICATIONS; X-RAY BRAGG DIFFRACTION IMAGINGRocking curve imaging (projection and section X-ray topography) has been used to study the generation and propagation of defects at the junctions between and above the seed crystals in mono-like silicon ingots. The images of different kinds of defects such as precipitates, dislocations and twins in the integrated intensity, full width at half-maximum and peak position maps resulting from the experiment have been studied. The qualitative and quantitative information that can be extracted from these maps, in particular the contrast of the images of the various defects, is discussed. These defects have a detrimental effect on solar cell efficiency and their detailed investigation allows clues to be obtained in order to improve the growth process. This work shows that synchrotron X-ray diffraction imaging techniques, because of their high angular resolution (<10−4°) and large field of view (several mm2), constitute a powerful tool for investigating the initial stages of growth of directionally solidified mono-like silicon.text/htmlCharacterization of defects in mono-like silicon for photovoltaic applications using X-ray Bragg diffraction imagingThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-16645research papers1600-5767med@iucr.org6541600-5767SynchWeb: a modern interface for ISPyBhttp://scripts.iucr.org/cgi-bin/paper?fs5101
SynchWeb is a modern interface to the ISPyB database. It significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography. It adds a variety of new features including project management, an integrated diffraction image viewer, and a map and model viewer, as well as displaying results from automated analysis pipelines. Virtually all aspects of an experiment can be monitored through the web browser and the success of each experiment can be evaluated.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Fisher, S.J.Levik, K.E.Williams, M.A.Ashton, A.W.McAuley, K.E.2015-04-25doi:10.1107/S1600576715004847International Union of CrystallographySynchWeb significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography.enDATA COLLECTION; REMOTE ACCESS; MACROMOLECULAR CRYSTALLOGRAPHYSynchWeb is a modern interface to the ISPyB database. It significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography. It adds a variety of new features including project management, an integrated diffraction image viewer, and a map and model viewer, as well as displaying results from automated analysis pipelines. Virtually all aspects of an experiment can be monitored through the web browser and the success of each experiment can be evaluated.text/htmlSynchWeb: a modern interface for ISPyBtext483http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-04-25927computer programs1600-5767med@iucr.org9321600-5767High-resolution characterization of the forbidden Si 200 and Si 222 reflectionsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?zr5001
The occurrence of the basis-forbidden Si 200 and Si 222 reflections in specular X-ray diffraction ω–2Θ scans is investigated in detail as a function of the in-plane sample orientation Φ. This is done for two different diffractometer types with low and high angular divergence perpendicular to the diffraction plane. It is shown that the reflections appear for well defined conditions as a result of multiple diffraction, and not only do the obtained peaks vary in intensity but additional features like shoulders or even subpeaks may occur within a 2Θ range of about ±2.5°. This has important consequences for the detection and verification of layer peaks in the corresponding angular range.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Zaumseil, P.2015-03-24doi:10.1107/S1600576715004732International Union of CrystallographyThe basis-forbidden Si 200 and Si 222 reflections are investigated in detail as a function of the in-plane sample orientation Φ and the divergence perpendicular to the diffraction plane of the used diffractometer. The results have important consequences for the detection of layer peaks near these reflections.enX-RAY DIFFRACTION; SILICON; FORBIDDEN REFLECTIONS; MULTIPLE DIFFRACTION; UMWEGANREGUNGThe occurrence of the basis-forbidden Si 200 and Si 222 reflections in specular X-ray diffraction ω–2Θ scans is investigated in detail as a function of the in-plane sample orientation Φ. This is done for two different diffractometer types with low and high angular divergence perpendicular to the diffraction plane. It is shown that the reflections appear for well defined conditions as a result of multiple diffraction, and not only do the obtained peaks vary in intensity but additional features like shoulders or even subpeaks may occur within a 2Θ range of about ±2.5°. This has important consequences for the detection and verification of layer peaks in the corresponding angular range.text/htmlHigh-resolution characterization of the forbidden Si 200 and Si 222 reflectionsThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-03-24528research papers1600-5767med@iucr.org5321600-5767Strain and dislocation gradients from diffraction. Edited by Rozaliya I. Barabash and Gene E. Ice. Imperial College Press, 2014. Price (hardcover) GBP 104. ISBN-978-1-908979-62-9.http://scripts.iucr.org/cgi-bin/paper?xo0008
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Gatti, R.2015-03-24doi:10.1107/S1600576715004525International Union of CrystallographyenBOOK REVIEWtext/htmlStrain and dislocation gradients from diffraction. Edited by Rozaliya I. Barabash and Gene E. Ice. Imperial College Press, 2014. Price (hardcover) GBP 104. ISBN-978-1-908979-62-9.text482Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-03-24619book reviews1600-5767med@iucr.org6191600-5767The fast azimuthal integration Python library: pyFAIhttp://scripts.iucr.org/cgi-bin/paper?fv5028
pyFAI is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.This article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ashiotis, G.Deschildre, A.Nawaz, Z.Wright, J.P.Karkoulis, D.Picca, F.E.Kieffer, J.2015-03-24doi:10.1107/S1600576715004306International Union of CrystallographyThis article details the geometry, peak-picking, calibration and integration procedures on multi- and many-core devices implemented in the Python library for high-performance azimuthal integration.enPOWDER DIFFRACTION; SMALL-ANGLE X-RAY SCATTERING; GEOMETRY CALIBRATION; DATA REDUCTION; IMAGE ANALYSIS; GPU PROGRAMMING; PYTHON; COMPUTER PROGRAMSpyFAI is an open-source software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments. It is written in Python (with binary submodules for improved performance), a language widely accepted and used by the scientific community today, which enables users to easily incorporate the pyFAI library into their processing pipeline. This article focuses on recent work, especially the ease of calibration, its accuracy and the execution speed for integration.This article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text/htmlThe fast azimuthal integration Python library: pyFAItext482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-03-24510research papers1600-5767med@iucr.org5191600-5767Quantitative X-ray phase contrast waveguide imaging of bacterial endosporesThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?zc5002
Quantitative waveguide-based X-ray phase contrast imaging has been carried out on the level of single, unstained, unsliced and freeze-dried bacterial cells of Bacillus thuringiensis and Bacillus subtilis using hard X-rays of 7.9 keV photon energy. The cells have been prepared in the metabolically dormant state of an endospore. The quantitative phase maps obtained by iterative phase retrieval using a modified hybrid input–output algorithm allow for mass and mass density determinations on the level of single individual endospores but include also large field of view investigations. Additionally, a direct reconstruction based on the contrast transfer function is investigated, and the two approaches are compared. Depending on the field of view and method, a resolution down to 65 nm was achieved at a maximum applied dose of below 5 × 105 Gy. Masses in the range of about ∼110–190 (20) fg for isolated endospores have been obtained.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Wilke, R.N.Hoppert, M.Krenkel, M.Bartels, M.Salditt, T.2015-03-24doi:10.1107/S1600576715003593International Union of CrystallographyQuantitative X-ray phase contrast imaging uniquely offers quantitative imaging information in terms of electron density maps allowing for mass and mass density determinations of soft biological samples (`weighing with light'). Here, it was carried out using coherent X-ray waveguide illumination, yielding values of the mass and mass density of freeze-dried bacterial endospores (Bacillus spp.).enPHASE RETRIEVAL; WAVEGUIDE IMAGING; CONTRAST TRANSFER FUNCTION; HOLOTOMOGRAPHY; BACILLUS THURINGIENSIS; BACILLUS SUBTILIS; ENDOSPORESQuantitative waveguide-based X-ray phase contrast imaging has been carried out on the level of single, unstained, unsliced and freeze-dried bacterial cells of Bacillus thuringiensis and Bacillus subtilis using hard X-rays of 7.9 keV photon energy. The cells have been prepared in the metabolically dormant state of an endospore. The quantitative phase maps obtained by iterative phase retrieval using a modified hybrid input–output algorithm allow for mass and mass density determinations on the level of single individual endospores but include also large field of view investigations. Additionally, a direct reconstruction based on the contrast transfer function is investigated, and the two approaches are compared. Depending on the field of view and method, a resolution down to 65 nm was achieved at a maximum applied dose of below 5 × 105 Gy. Masses in the range of about ∼110–190 (20) fg for isolated endospores have been obtained.text/htmlQuantitative X-ray phase contrast waveguide imaging of bacterial endosporesThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-03-24464research papers1600-5767med@iucr.org4761600-5767Powder diffraction in Bragg–Brentano geometry with straight linear detectorshttp://scripts.iucr.org/cgi-bin/paper?po5035
A common way of speeding up powder diffraction measurements is the use of one- or two-dimensional detectors. This usually goes hand in hand with worse resolution and asymmetric peak profiles. In this work the influence of a straight linear detector on the resolution function in the Bragg–Brentano focusing geometry is discussed. Because of the straight nature of most modern detectors geometrical defocusing occurs, which heavily influences the line shape of diffraction lines at low angles. An easy approach to limit the resolution-degrading effects is presented. The presented algorithm selects an adaptive range of channels of the linear detector at low angles, resulting in increased resolution. At higher angles the whole linear detector is used and the data collection remains fast. Using this algorithm a well behaved resolution function is obtained in the full angular range, whereas using the full linear detector the resolution function varies within one pattern, which hinders line-shape and Rietveld analysis.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Kriegner, D.Matěj, Z.Kužel, R.Holý, V.2015-03-24doi:10.1107/S1600576715003465International Union of CrystallographyThe influence of a straight linear detector on the powder diffraction signal in the Bragg–Brentano focusing geometry is presented. Recipes for how to limit resolution-degrading effects are developed.enPOWDER DIFFRACTION; BRAGG-BRENTANO; LINEAR DETECTOR; LINE SHAPE; RESOLUTION FUNCTIONA common way of speeding up powder diffraction measurements is the use of one- or two-dimensional detectors. This usually goes hand in hand with worse resolution and asymmetric peak profiles. In this work the influence of a straight linear detector on the resolution function in the Bragg–Brentano focusing geometry is discussed. Because of the straight nature of most modern detectors geometrical defocusing occurs, which heavily influences the line shape of diffraction lines at low angles. An easy approach to limit the resolution-degrading effects is presented. The presented algorithm selects an adaptive range of channels of the linear detector at low angles, resulting in increased resolution. At higher angles the whole linear detector is used and the data collection remains fast. Using this algorithm a well behaved resolution function is obtained in the full angular range, whereas using the full linear detector the resolution function varies within one pattern, which hinders line-shape and Rietveld analysis.text/htmlPowder diffraction in Bragg–Brentano geometry with straight linear detectorstext482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-03-24613laboratory notes1600-5767med@iucr.org6181600-5767Determination and mitigation of the uncertainty of neutron diffraction measurements of residual strain in large-grained polycrystalline materialhttp://scripts.iucr.org/cgi-bin/paper?ks5465
For large-grained samples it is advantageous to perform pairs of neutron diffraction measurements at the same spatial location but rotated 180° around the geometric centre of the gauge volume as a means of minimizing the scatter coming from the random positioning of grains within the gauge volume.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Holden, T.M.Traore, Y.James, J.Kelleher, J.Bouchard, P.J.2015-03-12doi:10.1107/S1600576715002757International Union of CrystallographyFor large-grained samples it is advantageous to perform pairs of neutron diffraction measurements at the same spatial location but rotated 180° around the geometric centre of the gauge volume as a means of minimizing the scatter coming from the random positioning of grains within the gauge volume.enMEASUREMENT UNCERTAINTY; NEUTRON DIFFRACTION; RESIDUAL STRAIN; POLYCRYSTALLINE MATERIALSFor large-grained samples it is advantageous to perform pairs of neutron diffraction measurements at the same spatial location but rotated 180° around the geometric centre of the gauge volume as a means of minimizing the scatter coming from the random positioning of grains within the gauge volume.text/htmlDetermination and mitigation of the uncertainty of neutron diffraction measurements of residual strain in large-grained polycrystalline materialtext482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-03-12582short communications1600-5767med@iucr.org5841600-5767Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY)http://scripts.iucr.org/cgi-bin/paper?ge5013
A high-brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed and optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization and the photon-counting PILATUS 2M detector enables the background-free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30–50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in-vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous-flow in-line sample purification and characterization, as well as an in-air capillary time-resolved stopped-flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high-throughput screening mode using sub-microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real-time assessments of overall parameters and the generation of low-resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high-throughput analysis, as well as time-resolved and screening experiments for novice and expert biological SAXS users.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Blanchet, C.E.Spilotros, A.Schwemmer, F.Graewert, M.A.Kikhney, A.Jeffries, C.M.Franke, D.Mark, D.Zengerle, R.Cipriani, F.Fiedler, S.Roessle, M.Svergun, D.I.2015-03-12doi:10.1107/S160057671500254XInternational Union of CrystallographyAn integrated environment for biological small-angle X-ray scattering (BioSAXS) at the high-brilliance P12 synchrotron beamline of the EMBL (DESY, Hamburg) allows for a broad range of solution scattering experiments. Automated hardware and software systems have been designed to ensure that data collection and processing are efficient, streamlined and user friendly.enBIOLOGICAL SMALL-ANGLE X-RAY SCATTERING; HIGH-BRILLIANCE P12 SYNCHROTRON BEAMLINE; AUTOMATED HARDWARE AND SOFTWARE SYSTEMSA high-brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed and optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization and the photon-counting PILATUS 2M detector enables the background-free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30–50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in-vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous-flow in-line sample purification and characterization, as well as an in-air capillary time-resolved stopped-flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high-throughput screening mode using sub-microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real-time assessments of overall parameters and the generation of low-resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high-throughput analysis, as well as time-resolved and screening experiments for novice and expert biological SAXS users.text/htmlVersatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY)text482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-03-12431research papers1600-5767med@iucr.org4431600-5767X-ray micro Laue diffraction tomography analysis of a solid oxide fuel cellThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).http://scripts.iucr.org/cgi-bin/paper?nb5139
The relevance of micro Laue diffraction tomography (µ-LT) to investigate heterogeneous polycrystalline materials has been studied. For this purpose, a multiphase solid oxide fuel cell (SOFC) electrode composite made of yttria-stabilized zirconia and nickel oxide phases, with grains of about a few micrometres in size, has been analyzed. In order to calibrate the Laue data and to test the technique's sensitivity limits, a monocrystalline germanium sample of about 8 × 4 µm in cross-section size has also been studied through µ-LT. The SOFC and germanium Laue diffraction pattern analyses are compared and discussed. The indexing procedure has been successfully applied for the analysis of the germanium Laue data, and the depth-resolved two-dimensional cartographies of the full deviatoric strain tensor components were obtained. The development and application of an original geometrical approach to analyze the SOFC Laue data allowed the authors to resolve grains with sizes of about 3 µm and to identify their individual Laue patterns; by indexing those Laue patterns, the crystalline phases and orientations of most of the grains identified through the geometrical approach could be resolved.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ferreira Sanchez, D.Villanova, J.Laurencin, J.Micha, J.-S.Montani, A.Gergaud, P.Bleuet, P.2015-02-21doi:10.1107/S1600576715002447International Union of CrystallographyThrough micro Laue tomography analysis, the depth-resolved cartographies (i) of NiO grains in a solid oxide fuel cell sample and (ii) of the full tensor of the deviatoric strain into a slice of a Ge sample are obtained.enX-RAY MICRO LAUE DIFFRACTION TOMOGRAPHY; SOLID OXIDE FUEL CELLSThe relevance of micro Laue diffraction tomography (µ-LT) to investigate heterogeneous polycrystalline materials has been studied. For this purpose, a multiphase solid oxide fuel cell (SOFC) electrode composite made of yttria-stabilized zirconia and nickel oxide phases, with grains of about a few micrometres in size, has been analyzed. In order to calibrate the Laue data and to test the technique's sensitivity limits, a monocrystalline germanium sample of about 8 × 4 µm in cross-section size has also been studied through µ-LT. The SOFC and germanium Laue diffraction pattern analyses are compared and discussed. The indexing procedure has been successfully applied for the analysis of the germanium Laue data, and the depth-resolved two-dimensional cartographies of the full deviatoric strain tensor components were obtained. The development and application of an original geometrical approach to analyze the SOFC Laue data allowed the authors to resolve grains with sizes of about 3 µm and to identify their individual Laue patterns; by indexing those Laue patterns, the crystalline phases and orientations of most of the grains identified through the geometrical approach could be resolved.text/htmlX-ray micro Laue diffraction tomography analysis of a solid oxide fuel cellThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014).text482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-02-21357research papers1600-5767med@iucr.org3641600-5767Crystallization dynamics and interface stability of strontium titanate thin films on siliconhttp://scripts.iucr.org/cgi-bin/paper?kc5002
Different physical vapor deposition methods have been used to fabricate strontium titanate thin films. Within the binary phase diagram of SrO and TiO2 the stoichiometry ranges from Ti rich to Sr rich, respectively. The crystallization of these amorphous SrTiO3 layers is investigated by in situ grazing-incidence X-ray diffraction using synchrotron radiation. The crystallization dynamics and evolution of the lattice constants as well as crystallite sizes of the SrTiO3 layers were determined for temperatures up to 1223 K under atmospheric conditions applying different heating rates. At approximately 473 K, crystallization of perovskite-type SrTiO3 is initiated for Sr-rich electron beam evaporated layers, whereas Sr-depleted sputter-deposited thin films crystallize at 739 K. During annealing, a significant diffusion of Si from the substrate into the SrTiO3 layers occurs in the case of Sr-rich composition. This leads to the formation of secondary silicate phases which are observed by X-ray diffraction, transmission electron microscopy and X-ray photoelectron spectroscopy.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Hanzig, F.Hanzig, J.Mehner, E.Richter, C.Veselý, J.Stöcker, H.Abendroth, B.Motylenko, M.Klemm, V.Novikov, D.Meyer, D.C.2015-03-12doi:10.1107/S160057671500240XInternational Union of CrystallographyNonstoichiometric SrTiO3 thin films were fabricated by different thin-film deposition methods. The impact on the oxide/silcon interface stability as well as the crystallization onset temperature is investigated.enSTRONTIUM TITANATE; THIN FILMS; SILICON SUBSTRATES; CRYSTALLIZATION DYNAMICS; INTERFACE STABILITYDifferent physical vapor deposition methods have been used to fabricate strontium titanate thin films. Within the binary phase diagram of SrO and TiO2 the stoichiometry ranges from Ti rich to Sr rich, respectively. The crystallization of these amorphous SrTiO3 layers is investigated by in situ grazing-incidence X-ray diffraction using synchrotron radiation. The crystallization dynamics and evolution of the lattice constants as well as crystallite sizes of the SrTiO3 layers were determined for temperatures up to 1223 K under atmospheric conditions applying different heating rates. At approximately 473 K, crystallization of perovskite-type SrTiO3 is initiated for Sr-rich electron beam evaporated layers, whereas Sr-depleted sputter-deposited thin films crystallize at 739 K. During annealing, a significant diffusion of Si from the substrate into the SrTiO3 layers occurs in the case of Sr-rich composition. This leads to the formation of secondary silicate phases which are observed by X-ray diffraction, transmission electron microscopy and X-ray photoelectron spectroscopy.text/htmlCrystallization dynamics and interface stability of strontium titanate thin films on silicontext482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-03-12393research papers1600-5767med@iucr.org4001600-5767Nebula: reconstruction and visualization of scattering data in reciprocal spacehttp://scripts.iucr.org/cgi-bin/paper?te5002
Two-dimensional solid-state X-ray detectors can now operate at considerable data throughput rates that allow full three-dimensional sampling of scattering data from extended volumes of reciprocal space within second to minute time­scales. For such experiments, simultaneous analysis and visualization allows for remeasurements and a more dynamic measurement strategy. A new software, Nebula, is presented. It efficiently reconstructs X-ray scattering data, generates three-dimensional reciprocal space data sets that can be visualized interactively, and aims to enable real-time processing in high-throughput measurements by employing parallel computing on commodity hardware.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Reiten, A.Chernyshov, D.Mathiesen, R.H.2015-02-21doi:10.1107/S1600576715001788International Union of CrystallographyA software to reconstruct and visualize diffuse scattering in three-dimensional reciprocal space using data from X-ray area detectors is presented.enDIFFUSE SCATTERING; DATA ANALYSIS AND VISUALIZATION; COMPUTER PROGRAMSTwo-dimensional solid-state X-ray detectors can now operate at considerable data throughput rates that allow full three-dimensional sampling of scattering data from extended volumes of reciprocal space within second to minute time­scales. For such experiments, simultaneous analysis and visualization allows for remeasurements and a more dynamic measurement strategy. A new software, Nebula, is presented. It efficiently reconstructs X-ray scattering data, generates three-dimensional reciprocal space data sets that can be visualized interactively, and aims to enable real-time processing in high-throughput measurements by employing parallel computing on commodity hardware.text/htmlNebula: reconstruction and visualization of scattering data in reciprocal spacetext482http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-02-21604computer programs1600-5767med@iucr.org6071600-5767In situ bending of an Au nanowire monitored by micro Laue diffractionhttp://scripts.iucr.org/cgi-bin/paper?nb5141
This articleThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014). reports on the first successful combination of micro Laue (µLaue) diffraction with an atomic force microscope for in situ nanomechanical tests of individual nanostructures. In situ three-point bending on self-suspended gold nanowires was performed on the BM32 beamline at the ESRF using a specially designed atomic force microscope. During the bending process of the self-suspended wire, the evolution of µLaue diffraction patterns was monitored, allowing for extraction of the bending angle of the nanowire. This bending compares well with finite element analysis taking into account elastic constant bulk values and geometric nonlinearities. This novel experimental setup opens promising perspectives for studying mechanical properties at the nanoscale.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Leclere, C.Cornelius, T.W.Ren, Z.Davydok, A.Micha, J.-S.Robach, O.Richter, G.Belliard, L.Thomas, O.2015-01-30doi:10.1107/S1600576715001107International Union of CrystallographyThe in situ three-point bending of a single self-suspended Au nanowire is visualized by micro Laue diffraction. The nanowire deflection is inferred from the displacement of Laue spots and it is well described by finite element analysis taking into account geometric nonlinearities and the elastic constants of bulk Au.enMICRO-BEAM LAUE DIFFRACTION; NANOMECHANICAL TESTING; AU NANOWIRESThis articleThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014). reports on the first successful combination of micro Laue (µLaue) diffraction with an atomic force microscope for in situ nanomechanical tests of individual nanostructures. In situ three-point bending on self-suspended gold nanowires was performed on the BM32 beamline at the ESRF using a specially designed atomic force microscope. During the bending process of the self-suspended wire, the evolution of µLaue diffraction patterns was monitored, allowing for extraction of the bending angle of the nanowire. This bending compares well with finite element analysis taking into account elastic constant bulk values and geometric nonlinearities. This novel experimental setup opens promising perspectives for studying mechanical properties at the nanoscale.text/htmlIn situ bending of an Au nanowire monitored by micro Laue diffractiontext1482015-01-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers291med@iucr.org2961600-5767Beyond the International Year of Crystallographyhttp://scripts.iucr.org/cgi-bin/paper?me0566
Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Allen, A.J.Hajdu, J.Kaysser-Pyzalla, A.R.2015-01-30doi:10.1107/S1600576715000916International Union of CrystallographyA new editorial from the three Main Editors of Journal of Applied Crystallography (JAC) updates authors and readers, alike, on current JAC developments.enEDITORIALtext/htmlBeyond the International Year of Crystallographytext1482015-01-30Journal of Applied CrystallographyCopyright (c) 2015 International Union of Crystallography1600-5767editorial1med@iucr.org21600-5767Structural investigations of the α12 Si–Ge superstructurehttp://scripts.iucr.org/cgi-bin/paper?zr5004
This articleThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014). reports the X-ray diffraction-based structural characterization of the α12 multilayer structure SiGe2Si2Ge2SiGe12 [d'Avezac, Luo, Chanier & Zunger (2012). Phys. Rev. Lett. 108, 027401], which is predicted to form a direct bandgap material. In particular, structural parameters of the superlattice such as thickness and composition as well as interface properties, are obtained. Moreover, it is found that Ge subsequently segregates into layers. These findings are used as input parameters for band structure calculations. It is shown that the direct bandgap properties depend very sensitively on deviations from the nominal structure, and only almost perfect structures can actually yield a direct bandgap. Photoluminescence emission possibly stemming from the superlattice structure is observed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Etzelstorfer, T.Ahmadpor Monazam, M.R.Cecchi, S.Kriegner, D.Chrastina, D.Gatti, E.Grilli, E.Rosemann, N.Chatterjee, S.Holý, V.Pezzoli, F.Isella, G.Stangl, J.2015-01-30doi:10.1107/S1600576715000849International Union of CrystallographyX-ray diffraction-based structural analysis results of possible direct bandgap Si/Ge superlattices composed of monolayer thin deposits are presented, together with theoretical predictions and first optical measurements.enX-RAY DIFFRACTION; SILICON WAFERS; DIRECT BANDGAP MATERIALS; SUPERLATTICE STRUCTUREThis articleThis article will form part of a virtual special issue of the journal, presenting some highlights of the 12th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP2014). reports the X-ray diffraction-based structural characterization of the α12 multilayer structure SiGe2Si2Ge2SiGe12 [d'Avezac, Luo, Chanier & Zunger (2012). Phys. Rev. Lett. 108, 027401], which is predicted to form a direct bandgap material. In particular, structural parameters of the superlattice such as thickness and composition as well as interface properties, are obtained. Moreover, it is found that Ge subsequently segregates into layers. These findings are used as input parameters for band structure calculations. It is shown that the direct bandgap properties depend very sensitively on deviations from the nominal structure, and only almost perfect structures can actually yield a direct bandgap. Photoluminescence emission possibly stemming from the superlattice structure is observed.text/htmlStructural investigations of the α12 Si–Ge superstructuretext1482015-01-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers262med@iucr.org2681600-5767The NeXus data formathttp://scripts.iucr.org/cgi-bin/paper?po5029
NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Könnecke, M.Akeroyd, F.A.Bernstein, H.J.Brewster, A.S.Campbell, S.I.Clausen, B.Cottrell, S.Hoffmann, J.U.Jemian, P.R.Männicke, D.Osborn, R.Peterson, P.F.Richter, T.Suzuki, J.Watts, B.Wintersberger, E.Wuttke, J.2015-01-30doi:10.1107/S1600576714027575International Union of CrystallographyA description is presented of the NeXus data format for X-ray and neutron scattering and muon spectroscopy.enNEXUS DATA FORMAT; DATA EXCHANGE; DATA ARCHIVING; PLATFORM-INDEPENDENT; HDF5NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.text/htmlThe NeXus data formattext1482015-01-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs301med@iucr.org3051600-5767An optical chopper for generation of short X-ray pulses to allow in-house time-resolved photocrystallography. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?he9669
In the paper by Kamiński et al. [J. Appl. Cryst. (2014), 47, 1765–1768], Jason B. Benedict is missing from the list of authors. The complete list of authors should be Radosław Kamiński, Jason B. Benedict, Gary Nottingham and Philip Coppens.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Kamiński, R.Benedict, J.B.Nottingham, G.Coppens, P.2015-02-01doi:10.1107/S1600576714026764International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2014), 47, 1765–1768.enTIME-RESOLVED X-RAY DIFFRACTION; X-RAY PULSES; PHOTOCRYSTALLOGRAPHY; OPTICAL CHOPPERS; CHOPPER ENCLOSURESIn the paper by Kamiński et al. [J. Appl. Cryst. (2014), 47, 1765–1768], Jason B. Benedict is missing from the list of authors. The complete list of authors should be Radosław Kamiński, Jason B. Benedict, Gary Nottingham and Philip Coppens.text/htmlAn optical chopper for generation of short X-ray pulses to allow in-house time-resolved photocrystallography. Corrigendumtext481Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-02-01addenda and errata1600-5767med@iucr.org1600-5767Elastic macro strain and stress determination by powder diffraction: spherical harmonics analysis starting from the Voigt model. Corrigendahttp://scripts.iucr.org/cgi-bin/paper?ks5461
Corrections to the paper by Popa, Balzar & Vogel [J. Appl. Cryst. (2014), 47, 154–159] are provided.Copyright (c) 2015 International Union of Crystallographyurn:issn:1600-5767Popa, N.C.Balzar, D.Vogel, S.C.2015-02-01doi:10.1107/S1600576714026673International Union of CrystallographyCorrections to the paper by Popa, Balzar & Vogel [J. Appl. Cryst. (2014), 47, 154–159] are provided.enSTRAIN; STRESS; TEXTURED POLYCRYSTALS; POWDER DIFFRACTION; SPHERICAL HARMONICSCorrections to the paper by Popa, Balzar & Vogel [J. Appl. Cryst. (2014), 47, 154–159] are provided.text/htmlElastic macro strain and stress determination by powder diffraction: spherical harmonics analysis starting from the Voigt model. Corrigendatext481Copyright (c) 2015 International Union of CrystallographyJournal of Applied Crystallography2015-02-01addenda and errata1600-5767med@iucr.org1600-5767Towards multi-order hard X-ray imaging with multilayer zone plateshttp://scripts.iucr.org/cgi-bin/paper?to5096
This article describes holographic imaging experiments using a hard X-ray multilayer zone plate (MZP) with an outermost zone width of 10 nm at a photon energy of 18 keV. An order-sorting aperture (OSA) is omitted and emulated during data analysis by a `software OSA'. Scanning transmission X-ray microscopy usually carried out in the focal plane is generalized to the holographic regime. The MZP focus is characterized by a three-plane phase-retrieval algorithm to an FWHM of 10 nm.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Osterhoff, M.Eberl, C.Döring, F.Wilke, R.N.Wallentin, J.Krebs, H.-U.Sprung, M.Salditt, T.2015-01-30doi:10.1107/S1600576714026016International Union of CrystallographyMultilayer zone plates can be used for holographic imaging without an order-sorting aperture.enX-RAY IMAGING; MULTILAYER ZONE PLATESThis article describes holographic imaging experiments using a hard X-ray multilayer zone plate (MZP) with an outermost zone width of 10 nm at a photon energy of 18 keV. An order-sorting aperture (OSA) is omitted and emulated during data analysis by a `software OSA'. Scanning transmission X-ray microscopy usually carried out in the focal plane is generalized to the holographic regime. The MZP focus is characterized by a three-plane phase-retrieval algorithm to an FWHM of 10 nm.text/htmlTowards multi-order hard X-ray imaging with multilayer zone platestext1482015-01-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers116med@iucr.org1241600-5767An X-ray diffractometer using mirage diffraction. Erratumhttp://scripts.iucr.org/cgi-bin/paper?to5104
Errors in the article by Fukamachi, Jongsukswat, Ju, Negishi, Hirano & Kawamura [J. Appl. Cryst. (2014), 47, 1267–1272] are corrected.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Fukamachi, T.Jongsukswat, S.Ju, D.Negishi, R.Hirano, K.Kawamura, T.2015-02-01doi:10.1107/S1600576714026028International Union of CrystallographyErrors in the article by Fukamachi, Jongsukswat, Ju, Negishi, Hirano & Kawamura [J. Appl. Cryst. (2014), 47, 1267–1272] are corrected.enMIRAGE DIFFRACTION; MIRAGE FRINGES; INTERFERENCE FRINGES; X-RAY DIFRACTOMETERS; MONOCHROMATORS; DYNAMICAL THEORY OF X-RAY DIFFRACTIONErrors in the article by Fukamachi, Jongsukswat, Ju, Negishi, Hirano & Kawamura [J. Appl. Cryst. (2014), 47, 1267–1272] are corrected.text/htmlAn X-ray diffractometer using mirage diffraction. Erratumtext481http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2015-02-01addenda and errata1600-5767med@iucr.org1600-5767Computing stoichiometric molecular composition from crystal structureshttp://scripts.iucr.org/cgi-bin/paper?kk5188
Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Gražulis, S.Merkys, A.Vaitkus, A.Okulič-Kazarinas, M.2015-01-30doi:10.1107/S1600576714025904International Union of CrystallographyAn algorithm to compute stoichiometrically correct molecular formulae from crystal structures is proposed. The algorithm's output is suitable for high-volume automated searches in chemical databases and for linking crystallographic and chemical information.enMOLECULAR STRUCTURE; MULTIMOLECULAR ENSEMBLESCrystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases.text/htmlComputing stoichiometric molecular composition from crystal structurestext1482015-01-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers85med@iucr.org911600-5767John Ian Langford (1935–2013)http://scripts.iucr.org/cgi-bin/paper?es0409
Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767, R.J.Louër, D.Mittemeijer, E.J.Scardi, P.2014-11-27doi:10.1107/S1600576714025527International Union of CrystallographyObituary for John Ian Langford.enOBITUARYtext/htmlJohn Ian Langford (1935–2013)text6472014-11-27Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767crystallographers2114med@iucr.org21151600-5767New enhanced tool for neutron spin echo spectroscopyhttp://scripts.iucr.org/cgi-bin/paper?aj5249
urn:issn:1600-5767Mezei, F.2014-11-27doi:10.1107/S1600576714024996International Union of CrystallographySome recent developments in neutron spin echo spectroscopy are discussed.enNEUTRON SPIN ECHO SPECTROSCOPY; PHONON LINEWIDTH MEASUREMENTtext/htmlNew enhanced tool for neutron spin echo spectroscopytext6472014-11-27Journal of Applied Crystallography1600-5767scientific commentaries1807med@iucr.org18081600-5767Comparison of silver and molybdenum microfocus X-ray sources for single-crystal structure determinationhttp://scripts.iucr.org/cgi-bin/paper?aj5242
The quality of diffraction data obtained using silver and molybdenum microsources has been compared for six model compounds with a wide range of absorption factors. The experiments were performed on two 30 W air-cooled Incoatec IµS microfocus sources with multilayer optics mounted on a Bruker D8 goniometer with a SMART APEX II CCD detector. All data were analysed, processed and refined using standard Bruker software. The results show that Ag Kα radiation can be beneficial when heavy elements are involved. A numerical absorption correction based on the positions and indices of the crystal faces is shown to be of limited use for the highly focused microsource beams, presumably because the assumption that the crystal is completely bathed in a (top-hat profile) beam of uniform intensity is no longer valid. Fortunately the empirical corrections implemented in SADABS, although originally intended as a correction for absorption, also correct rather well for the variations in the effective volume of the crystal irradiated. In three of the cases studied (two Ag and one Mo) the final SHELXL R1 against all data after application of empirical corrections implemented in SADABS was below 1%. Since such corrections are designed to optimize the agreement of the intensities of equivalent reflections with different paths through the crystal but the same Bragg 2θ angles, a further correction is required for the 2θ dependence of the absorption. For this, SADABS uses the transmission factor of a spherical crystal with a user-defined value of μr (where μ is the linear absorption coefficient and r is the effective radius of the crystal); the best results are obtained when r is biased towards the smallest crystal dimension. The results presented here suggest that the IUCr publication requirement that a numerical absorption correction must be applied for strongly absorbing crystals is in need of revision.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Krause, L.Herbst-Irmer, R.Sheldrick, G.M.Stalke, D.2015-01-30doi:10.1107/S1600576714022985International Union of CrystallographyA detailed comparison of single-crystal diffraction data collected with Ag Kα and Mo Kα microsources (IµS) indicates that the Ag Kα data are better when absorption is significant. Empirical corrections intended to correct for absorption also correct well for the effects of the highly focused IµS beams.enMICROFOCUS X-RAY SOURCES; SINGLE-CRYSTAL STRUCTURE DETERMINATION; ABSORPTION CORRECTIONThe quality of diffraction data obtained using silver and molybdenum microsources has been compared for six model compounds with a wide range of absorption factors. The experiments were performed on two 30 W air-cooled Incoatec IµS microfocus sources with multilayer optics mounted on a Bruker D8 goniometer with a SMART APEX II CCD detector. All data were analysed, processed and refined using standard Bruker software. The results show that Ag Kα radiation can be beneficial when heavy elements are involved. A numerical absorption correction based on the positions and indices of the crystal faces is shown to be of limited use for the highly focused microsource beams, presumably because the assumption that the crystal is completely bathed in a (top-hat profile) beam of uniform intensity is no longer valid. Fortunately the empirical corrections implemented in SADABS, although originally intended as a correction for absorption, also correct rather well for the variations in the effective volume of the crystal irradiated. In three of the cases studied (two Ag and one Mo) the final SHELXL R1 against all data after application of empirical corrections implemented in SADABS was below 1%. Since such corrections are designed to optimize the agreement of the intensities of equivalent reflections with different paths through the crystal but the same Bragg 2θ angles, a further correction is required for the 2θ dependence of the absorption. For this, SADABS uses the transmission factor of a spherical crystal with a user-defined value of μr (where μ is the linear absorption coefficient and r is the effective radius of the crystal); the best results are obtained when r is biased towards the smallest crystal dimension. The results presented here suggest that the IUCr publication requirement that a numerical absorption correction must be applied for strongly absorbing crystals is in need of revision.text/htmlComparison of silver and molybdenum microfocus X-ray sources for single-crystal structure determinationtext1482015-01-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers3med@iucr.org101600-5767Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control systemhttp://scripts.iucr.org/cgi-bin/paper?he5668
The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates a collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Pothineni, S.B.Venugopalan, N.Ogata, C.M.Hilgart, M.C.Stepanov, S.Sanishvili, R.Becker, M.Winter, G.Sauter, N.K.Smith, J.L.Fischetti, R.F.2014-11-18doi:10.1107/S1600576714022730International Union of CrystallographySingle- and multi-crystal data collection strategy and automated data processing have been tightly integrated into the JBluIce graphical user interface. Grid Engine is used to distribute these processes into multiple workstations to make efficient use of all available computing resources.enAUTOMATED DATA PROCESSING; MULTI-CRYSTAL DATA COLLECTION STRATEGIES; X-RAY CRYSTALLOGRAPHY; GRID ENGINEThe calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates a collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce.text/htmlTightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control systemtext6472014-11-18Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1992med@iucr.org19991600-5767Elastic strain and stress determination by Rietveld refinement: generalized treatment for textured polycrystals for all Laue classes. Second corrigendumhttp://scripts.iucr.org/cgi-bin/paper?ks5454
Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Popa, N.C.Balzar, D.2014-11-04doi:10.1107/S1600576714022109International Union of CrystallographyThis corrigendum replaces the first corrigendum [Popa & Balzar (2012). 45, 838–839], which was published to correct errors in the article by Popa & Balzar [J. Appl. Cryst. (2001), 34, 187–195].enSTRESS; STRAIN; TEXTURE; POLYCRYSTALS; LAUE CLASSES; RIETVELD REFINEMENTtext/htmlElastic strain and stress determination by Rietveld refinement: generalized treatment for textured polycrystals for all Laue classes. Second corrigendumtext6472014-11-04Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767addenda and errata2113med@iucr.org21131600-5767CREDO: a new general-purpose laboratory instrument for small-angle X-ray scatteringhttp://scripts.iucr.org/cgi-bin/paper?ks5446
The details of a newly constructed small-angle X-ray scattering instrument are presented. The geometry of the instrument is highly customizable, enabling it to address vastly different experimental situations from academic research to industrial problems. The high degree of motorization and automation compared to conventional laboratory-scale SAXS instruments facilitates the alignment and daily use. Data reduction routines are incorporated in the instrument control software, yielding fully corrected and calibrated results promptly after the end of measurements. Optimization of the flux versus resolution balance can be done routinely for each measurement task. A wide, continuous range of q = 4πsinθ/λ can be reached, from below 0.02 nm−1 up to 30 nm−1, corresponding to periodic distances of ca 350 nm down to 0.2 nm. A few representative results obtained from samples of different research fields demonstrate the versatility of the instrument. Scattering curves are routinely calibrated into absolute units using a glassy carbon secondary standard. More information and recent developments can be found on the web page of the instrument at http://credo.ttk.mta.hu.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Wacha, A.Varga, Z.Bóta, A.2014-09-30doi:10.1107/S1600576714019918International Union of CrystallographyA new custom-built and highly flexible small-angle X-ray scattering instrument is presented.enSMALL-ANGLE X-RAY SCATTERING (SAXS); INSTRUMENTATIONThe details of a newly constructed small-angle X-ray scattering instrument are presented. The geometry of the instrument is highly customizable, enabling it to address vastly different experimental situations from academic research to industrial problems. The high degree of motorization and automation compared to conventional laboratory-scale SAXS instruments facilitates the alignment and daily use. Data reduction routines are incorporated in the instrument control software, yielding fully corrected and calibrated results promptly after the end of measurements. Optimization of the flux versus resolution balance can be done routinely for each measurement task. A wide, continuous range of q = 4πsinθ/λ can be reached, from below 0.02 nm−1 up to 30 nm−1, corresponding to periodic distances of ca 350 nm down to 0.2 nm. A few representative results obtained from samples of different research fields demonstrate the versatility of the instrument. Scattering curves are routinely calibrated into absolute units using a glassy carbon secondary standard. More information and recent developments can be found on the web page of the instrument at http://credo.ttk.mta.hu.text/htmlCREDO: a new general-purpose laboratory instrument for small-angle X-ray scatteringtext5472014-09-30Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767research papers1749med@iucr.org17541600-5767A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the new DPDAK package to small-angle X-ray scattering and grazing-incidence small-angle X-ray scatteringhttp://scripts.iucr.org/cgi-bin/paper?rw5077
X-ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open-source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one- or two-dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software, DPDAK (directly programmable data analysis kit), is based on a plug-in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use of DPDAK for on- and offline analysis of scanning small-angle X-ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing-incidence SAXS data. In addition to a comparison with existing software packages, the structure of DPDAK and the possibilities and limitations are discussed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Benecke, G.Wagermaier, W.Li, C.Schwartzkopf, M.Flucke, G.Hoerth, R.Zizak, I.Burghammer, M.Metwalli, E.Müller-Buschbaum, P.Trebbin, M.Förster, S.Paris, O.Roth, S.V.Fratzl, P.2014-09-30doi:10.1107/S1600576714019773International Union of CrystallographyDPDAK is a software for simple and fast on- and offline reduction and analysis of X-ray scattering data. It is an open-source software with a plug-in structure allowing tailored extensions.enSMALL-ANGLE X-RAY SCATTERING; GRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING; DATA REDUCTION; DATA ANALYSIS; COMPUTER PROGRAMSX-ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open-source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one- or two-dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software, DPDAK (directly programmable data analysis kit), is based on a plug-in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use of DPDAK for on- and offline analysis of scanning small-angle X-ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing-incidence SAXS data. In addition to a comparison with existing software packages, the structure of DPDAK and the possibilities and limitations are discussed.text/htmlA customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the new DPDAK package to small-angle X-ray scattering and grazing-incidence small-angle X-ray scatteringtext5472014-09-30Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1797med@iucr.org18031600-5767Transmission electron microscopy analysis of the crystallography of precipitates in Mg–Sn alloys aged at high temperatureshttp://scripts.iucr.org/cgi-bin/paper?nb5116
The crystallographic orientation relationships (ORs) of precipitated β-Mg2Sn particles in Mg–9.76 wt% Sn alloy aged at 573 K for 5 h, corresponding to its peak hardness, were investigated by advanced transmission electron microscopy (TEM). OR-3 of (110)β//(0001)α and [\overline 111]β//[1\overline 210]α and OR-4 of (110)β//(0001)α and [001]β//[2\overline 1\overline 10]α are the key ORs of β-Mg2Sn particles in the alloy. The proportions of β-Mg2Sn particles exhibiting OR-3 and OR-4 were determined as 75.1 and 24.3%, respectively. Crystallographic factors determined the predominance of OR-3 in the precipitated β-Mg2Sn particles. This mechanism was analyzed by a three-dimensional invariant line model constructed using a transformation matrix in reciprocal space. Models of the interface of precipitated β-Mg2Sn and the α-Mg matrix were constructed via high-resolution TEM and atomic resolution high-angle annular dark-field scanning TEM.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Nie, X.Guan, Y.Zhao, D.Liu, Y.Gui, J.Li, L.Wang, J.2014-09-30doi:10.1107/S160057671401958XInternational Union of CrystallographyThe crystallographic orientation relationships of precipitated β-Mg2Sn particles in Mg–9.76 wt% Sn alloy aged at 573 K for 5 h were investigated by advanced transmission electron microscopy (TEM). Models of the interface of precipitated β-Mg2Sn and the α-Mg matrix were constructed via high-resolution TEM and atomic resolution high-angle annular dark-field scanning TEM.enCRYSTALLOGRAPHIC ORIENTATION RELATIONSHIPS; PRECIPITATES; MAGNESIUM-BASED ALLOYSThe crystallographic orientation relationships (ORs) of precipitated β-Mg2Sn particles in Mg–9.76 wt% Sn alloy aged at 573 K for 5 h, corresponding to its peak hardness, were investigated by advanced transmission electron microscopy (TEM). OR-3 of (110)β//(0001)α and [\overline 111]β//[1\overline 210]α and OR-4 of (110)β//(0001)α and [001]β//[2\overline 1\overline 10]α are the key ORs of β-Mg2Sn particles in the alloy. The proportions of β-Mg2Sn particles exhibiting OR-3 and OR-4 were determined as 75.1 and 24.3%, respectively. Crystallographic factors determined the predominance of OR-3 in the precipitated β-Mg2Sn particles. This mechanism was analyzed by a three-dimensional invariant line model constructed using a transformation matrix in reciprocal space. Models of the interface of precipitated β-Mg2Sn and the α-Mg matrix were constructed via high-resolution TEM and atomic resolution high-angle annular dark-field scanning TEM.text/htmlTransmission electron microscopy analysis of the crystallography of precipitates in Mg–Sn alloys aged at high temperaturestext5472014-09-30Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767research papers1729med@iucr.org17351600-5767SynchLink: an iOS app for ISPyBhttp://scripts.iucr.org/cgi-bin/paper?he5667
The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now provided via an iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Ginn, H.M.Mostefaoui, G.K.Levik, K.E.Grimes, J.M.Walsh, M.A.Ashton, A.W.Stuart, D.I.2014-09-04doi:10.1107/S1600576714017531International Union of CrystallographyAn iOS app has been developed as a front end to ISPyB, a laboratory information system for macromolecular crystallography synchrotron beamlines.enREMOTE DATA COLLECTION; SYNCHROTRON RADIATION; MACROMOLECULAR CRYSTALLOGRAPHY; LABORATORY INFORMATION MANAGEMENT SYSTEMS (LIMS)The macromolecular crystallography (MX) user experience at synchrotron radiation facilities continues to evolve, with the impact of developments in X-ray detectors, computer hardware and automation methods making it possible for complete data sets to be collected on timescales of tens of seconds. Data can be reduced in a couple of minutes and in favourable cases structures solved and refined shortly after. The information-rich database ISPyB, automatically populated by data acquisition software, data processing and structure solution pipelines at the Diamond Light Source beamlines, allows users to automatically track MX experiments in real time. In order to improve the synchrotron users' experience, efficient access to the data contained in ISPyB is now provided via an iOS 6.0+ app for iPhones and iPads. This provides users, both local and remote, with a succinct summary of data collection, visualization of diffraction images and crystals, and key metrics for data quality in real time.text/htmlSynchLink: an iOS app for ISPyBtext5472014-09-04Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1781med@iucr.org17831600-5767Neutron and X-ray diffraction study of ferrite nanocrystals obtained by microwave-assisted growth. A structural comparison with the thermal synthetic route. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?kk9153
In the paper by Solano et al. [J. Appl. Cryst. (2014), 47, 414–420], Inés Puente Orench is missing from the list of authors. The complete list of authors should be Eduardo Solano, Carlos Frontera, Inés Puente Orench, Teresa Puig, Xavier Obradors, Susagna Ricart and Josep Ros.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Solano, E.Frontera, C.Puente Orench, I.Puig, T.Obradors, X.Ricart, S.Ros, J.2014-08-01doi:10.1107/S1600576714017452International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2014), 47, 414–420.enPOWDER DIFFRACTION; FERRITE; MICROWAVES; NANOPARTICLES; NEUTRONS; STRUCTURE; SYNTHESISIn the paper by Solano et al. [J. Appl. Cryst. (2014), 47, 414–420], Inés Puente Orench is missing from the list of authors. The complete list of authors should be Eduardo Solano, Carlos Frontera, Inés Puente Orench, Teresa Puig, Xavier Obradors, Susagna Ricart and Josep Ros.text/htmlNeutron and X-ray diffraction study of ferrite nanocrystals obtained by microwave-assisted growth. A structural comparison with the thermal synthetic route. Corrigendumtext474http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2014-08-011478addenda and errata1600-5767med@iucr.org14781600-5767Promising times for small-angle neutron scatteringhttp://scripts.iucr.org/cgi-bin/paper?aj5241
urn:issn:1600-5767Andersen, K.H.Barker, J.G.2014-07-31doi:10.1107/S1600576714017233International Union of CrystallographyPlease provide a synopsis (of not more than two sentences) to appear in the Contents listing of the journal.enVERY SMALL ANGLE NEUTRON SCATTERING (VSANS); SMALL-ANGLE NEUTRON SCATTERING (SANS); MULTIPLE BEAMS; INSTRUMENT SIMULATION; NEUTRON OPTICStext/htmlPromising times for small-angle neutron scatteringtext4472014-07-31Journal of Applied Crystallography1600-5767scientific commentaries1163med@iucr.org11641600-5767Mass-fractal growth in niobia/silsesquioxane mixtures: a small-angle X-ray scattering studyhttp://scripts.iucr.org/cgi-bin/paper?vh5007
The nucleation and growth of niobium pentaethoxide (NPE)-derived clusters in ethanol, through acid-catalyzed hydrolysis/condensation in the presence and absence of the silsesquioxane 1,2-bis(triethoxysilyl)ethane (BTESE), was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures. At 298–313 K in the absence of BTESE the data indicated the development of relatively monodisperse NPE-derived structures with self-preserving polydispersity during growth. The growth exponent was consistent with irreversible diffusion-limited cluster agglomeration. At 333 K the growth exponent was characteristic for fast-gelling reaction-limited cluster agglomeration. The reaction yielded substantially higher degrees of polydispersity. In the presence of BTESE the growth exponents were substantially smaller. The smaller growth exponent in this case is not consistent with irreversible Smoluchowski-type agglomeration. Instead, reversible Lifshitz–Slyozov-type agglomeration seems to be more consistent with the experimental data.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Besselink, R.Elshof, J.E. ten2014-09-04doi:10.1107/S1600576714017105International Union of CrystallographyThe nucleation and growth of niobium pentaethoxide-derived clusters in ethanol was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures.enMASS-FRACTAL GROWTH; NIOBIA; SILSESQUIOXANE; SMALL-ANGLE X-RAY SCATTERINGThe nucleation and growth of niobium pentaethoxide (NPE)-derived clusters in ethanol, through acid-catalyzed hydrolysis/condensation in the presence and absence of the silsesquioxane 1,2-bis(triethoxysilyl)ethane (BTESE), was monitored at 298–333 K by small-angle X-ray scattering. The data were analyzed with a newly derived model for polydisperse mass-fractal-like structures. At 298–313 K in the absence of BTESE the data indicated the development of relatively monodisperse NPE-derived structures with self-preserving polydispersity during growth. The growth exponent was consistent with irreversible diffusion-limited cluster agglomeration. At 333 K the growth exponent was characteristic for fast-gelling reaction-limited cluster agglomeration. The reaction yielded substantially higher degrees of polydispersity. In the presence of BTESE the growth exponents were substantially smaller. The smaller growth exponent in this case is not consistent with irreversible Smoluchowski-type agglomeration. Instead, reversible Lifshitz–Slyozov-type agglomeration seems to be more consistent with the experimental data.text/htmlMass-fractal growth in niobia/silsesquioxane mixtures: a small-angle X-ray scattering studytext5472014-09-04Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1606med@iucr.org16131600-5767Time-resolved coherent X-ray diffraction imaging of surface acoustic waveshttp://scripts.iucr.org/cgi-bin/paper?rg5067
Time-resolved coherent X-ray diffraction experiments of standing surface acoustic waves, illuminated under grazing incidence by a nanofocused synchrotron beam, are reported. The data have been recorded in stroboscopic mode at controlled and varied phase between the acoustic frequency generator and the synchrotron bunch train. At each time delay (phase angle), the coherent far-field diffraction pattern in the small-angle regime is inverted by an iterative algorithm to yield the local instantaneous surface height profile along the optical axis. The results show that periodic nanoscale dynamics can be imaged at high temporal resolution in the range of 50 ps (pulse length).http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Nicolas, J.-D.Reusch, T.Osterhoff, M.Sprung, M.Schúlein, F.J.R.Krenner, H.J.Wixforth, A.Salditt, T.2014-09-04doi:10.1107/S1600576714016896International Union of CrystallographyThe time-dependent one-dimensional height profile of a standing surface acoustic wave on an LiNbO3 substrate has been reconstructed from stroboscopically recorded coherent grazing-incidence small-angle diffraction patterns.enCOHERENT X-RAY DIFFRACTION IMAGING; SURFACE ACOUSTIC WAVES; NANOSTRUCTURETime-resolved coherent X-ray diffraction experiments of standing surface acoustic waves, illuminated under grazing incidence by a nanofocused synchrotron beam, are reported. The data have been recorded in stroboscopic mode at controlled and varied phase between the acoustic frequency generator and the synchrotron bunch train. At each time delay (phase angle), the coherent far-field diffraction pattern in the small-angle regime is inverted by an iterative algorithm to yield the local instantaneous surface height profile along the optical axis. The results show that periodic nanoscale dynamics can be imaged at high temporal resolution in the range of 50 ps (pulse length).text/htmlTime-resolved coherent X-ray diffraction imaging of surface acoustic wavestext5472014-09-04Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1596med@iucr.org16051600-5767The geometry of Niggli reduction: BGAOL – embedding Niggli reduction and analysis of boundaries. Erratumhttp://scripts.iucr.org/cgi-bin/paper?kk9144
Ambiguities in the article by Andrews & Bernstein [J. Appl. Cryst. (2014), 47, 346–359] are clarified.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Andrews, L.C.Bernstein, H.J.2014-07-19doi:10.1107/S1600576714014460International Union of CrystallographyAmbiguities in the article by Andrews & Bernstein [J. Appl. Cryst. (2014), 47, 346–359] are clarified.enNIGGLI REDUCTION; BRAVAIS LATTICE DETERMINATION; COMPUTER PROGRAMSAmbiguities in the article by Andrews & Bernstein [J. Appl. Cryst. (2014), 47, 346–359] are clarified.text/htmlThe geometry of Niggli reduction: BGAOL – embedding Niggli reduction and analysis of boundaries. Erratumtext4472014-07-19Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767addenda and errata1477med@iucr.org14771600-5767All-diamond optical assemblies for a beam-multiplexing X-ray monochromator at the Linac Coherent Light Sourcehttp://scripts.iucr.org/cgi-bin/paper?nb5110
A double-crystal diamond (111) monochromator recently implemented at the Linac Coherent Light Source (LCLS) enables splitting of the primary X-ray beam into a pink (transmitted) and a monochromatic (reflected) branch. The first monochromator crystal, with a thickness of ∼100 µm, provides sufficient X-ray transmittance to enable simultaneous operation of two beamlines. This article reports the design, fabrication and X-ray characterization of the first and second (300 µm-thick) crystals utilized in the monochromator and the optical assemblies holding these crystals. Each crystal plate has a region of about 5 × 2 mm with low defect concentration, sufficient for use in X-ray optics at the LCLS. The optical assemblies holding the crystals were designed to provide mounting on a rigid substrate and to minimize mounting-induced crystal strain. The induced strain was evaluated using double-crystal X-ray topography and was found to be small over the 5 × 2 mm working regions of the crystals.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Stoupin, S.Terentyev, S.A.Blank, V.D.Shvyd'ko, Y.V.Goetze, K.Assoufid, L.Polyakov, S.N.Kuznetsov, M.S.Kornilov, N.V.Katsoudas, J.Alonso-Mori, R.Chollet, M.Feng, Y.Glownia, J.M.Lemke, H.Robert, A.Sikorski, M.Song, S.Zhu, D.2014-08-01doi:10.1107/S1600576714013028International Union of CrystallographyAll-diamond optical assemblies holding state-of-the-art type IIa diamond crystals enable the construction of a beam-multiplexing X-ray double-crystal monochromator for hard X-ray free-electron lasers. Details on the design, fabrication and X-ray diffraction characterization of the assemblies are reported.enDIAMOND; X-RAY MONOCHROMATORS; BEAM MULTIPLEXINGA double-crystal diamond (111) monochromator recently implemented at the Linac Coherent Light Source (LCLS) enables splitting of the primary X-ray beam into a pink (transmitted) and a monochromatic (reflected) branch. The first monochromator crystal, with a thickness of ∼100 µm, provides sufficient X-ray transmittance to enable simultaneous operation of two beamlines. This article reports the design, fabrication and X-ray characterization of the first and second (300 µm-thick) crystals utilized in the monochromator and the optical assemblies holding these crystals. Each crystal plate has a region of about 5 × 2 mm with low defect concentration, sufficient for use in X-ray optics at the LCLS. The optical assemblies holding the crystals were designed to provide mounting on a rigid substrate and to minimize mounting-induced crystal strain. The induced strain was evaluated using double-crystal X-ray topography and was found to be small over the 5 × 2 mm working regions of the crystals.text/htmlAll-diamond optical assemblies for a beam-multiplexing X-ray monochromator at the Linac Coherent Light Sourcetext4472014-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1329med@iucr.org13361600-5767An X-ray diffractometer using mirage diffractionhttp://scripts.iucr.org/cgi-bin/paper?to5063
Some characteristics are reported of a triple-crystal diffractometer with a (+, −, +) setting of Si(220) using mirage diffraction. The first crystal is flat, while the second and third crystals are bent. Basically, the first crystal is used as a collimator, the second as a monochromator and the third as the sample. The third crystal also works as an analyzer. The advantages of this diffractometer are that its setup is easy, its structure is simple, the divergence angle from the second crystal is small and the energy resolution of the third crystal is high, of the order of sub-meV.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Fukamachi, T.Jongsukswat, S.Ju, D.Negishi, R.Hirano, K.Kawamura, T.2014-07-19doi:10.1107/S1600576714012114International Union of CrystallographySome characteristics are reported of a triple-crystal diffractometer with a (+, −, +) setting of Si(220) using mirage diffraction. The advantages of this diffractometer are that its setup is easy, its structure is simple, the divergence angle from the second crystal is small and the energy resolution of the third crystal is very high.enMIRAGE DIFFRACTION; MIRAGE FRINGES; INTERFERENCE FRINGES; X-RAY DIFRACTOMETERS; MONOCHROMATORS; DYNAMICAL THEORY OF X-RAY DIFFRACTIONSome characteristics are reported of a triple-crystal diffractometer with a (+, −, +) setting of Si(220) using mirage diffraction. The first crystal is flat, while the second and third crystals are bent. Basically, the first crystal is used as a collimator, the second as a monochromator and the third as the sample. The third crystal also works as an analyzer. The advantages of this diffractometer are that its setup is easy, its structure is simple, the divergence angle from the second crystal is small and the energy resolution of the third crystal is high, of the order of sub-meV.text/htmlAn X-ray diffractometer using mirage diffractiontext4472014-07-19Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1267med@iucr.org12721600-5767dxtbx: the diffraction experiment toolboxhttp://scripts.iucr.org/cgi-bin/paper?jo5001
Data formats for recording X-ray diffraction data continue to evolve rapidly to accommodate new detector technologies developed in response to more intense light sources. Processing the data from single-crystal X-ray diffraction experiments therefore requires the ability to read, and correctly interpret, image data and metadata from a variety of instruments employing different experimental representations. Tools that have previously been developed to address this problem have been limited either by a lack of extensibility or by inconsistent treatment of image metadata. The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user-extensible approach to reading the data files. The library is written in a mixture of C++ and Python and is distributed as part of the cctbx under an open-source licence at http://cctbx.sourceforge.net.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Parkhurst, J.M.Brewster, A.S.Fuentes-Montero, L.Waterman, D.G.Hattne, J.Ashton, A.W.Echols, N.Evans, G.Sauter, N.K.Winter, G.2014-07-19doi:10.1107/S1600576714011996International Union of CrystallographyA Python/C++ library for reading image data and experimental geometry for X-ray diffraction experiments from arbitrary data sources is presented.enSINGLE-CRYSTAL X-RAY DIFFRACTION; DATA PROCESSING; COMPUTER PROGRAMSData formats for recording X-ray diffraction data continue to evolve rapidly to accommodate new detector technologies developed in response to more intense light sources. Processing the data from single-crystal X-ray diffraction experiments therefore requires the ability to read, and correctly interpret, image data and metadata from a variety of instruments employing different experimental representations. Tools that have previously been developed to address this problem have been limited either by a lack of extensibility or by inconsistent treatment of image metadata. The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user-extensible approach to reading the data files. The library is written in a mixture of C++ and Python and is distributed as part of the cctbx under an open-source licence at http://cctbx.sourceforge.net.text/htmldxtbx: the diffraction experiment toolboxtext4472014-07-19Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1459med@iucr.org14651600-5767Simple and efficient modifications of well known techniques for reliable growth of high-quality crystals of small bioorganic moleculeshttp://scripts.iucr.org/cgi-bin/paper?kk5169
A number of modifications to traditional techniques are suggested in order to overcome problems that frequently arise when growing crystals from solution. These improvements, and their combination, help to avoid problems such as poor nucleation, the spontaneous precipitation of many poor-quality small powder-like crystals, crystals adhering to the crystallization vessel or to each other, and chemical degradation of the solution. The proposed techniques can be used to crystallize desirable metastable polymorphs reliably. None of the suggested methods demands the usage of any special or expensive equipment, or specific skills, and they can be implemented in the chemistry curriculum even at secondary school level. Examples are given for the crystallization of small organic molecules such as carboxylic acids, amino acids, pharmaceuticals etc., but the same techniques are applicable to other classes of compound.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Rychkov, D.A.Arkhipov, S.G.Boldyreva, E.V.2014-06-14doi:10.1107/S1600576714011273International Union of CrystallographySimple and efficient techniques are suggested to overcome problems that frequently arise when growing single crystals from solution.enCRYSTAL GROWTH FROM SOLUTION; X-RAY DIFFRACTION; RAMAN SPECTROSCOPY; CONTROL OF NUCLEATION; CONTROL OF NUCLEI GROWTH; SEEDINGA number of modifications to traditional techniques are suggested in order to overcome problems that frequently arise when growing crystals from solution. These improvements, and their combination, help to avoid problems such as poor nucleation, the spontaneous precipitation of many poor-quality small powder-like crystals, crystals adhering to the crystallization vessel or to each other, and chemical degradation of the solution. The proposed techniques can be used to crystallize desirable metastable polymorphs reliably. None of the suggested methods demands the usage of any special or expensive equipment, or specific skills, and they can be implemented in the chemistry curriculum even at secondary school level. Examples are given for the crystallization of small organic molecules such as carboxylic acids, amino acids, pharmaceuticals etc., but the same techniques are applicable to other classes of compound.text/htmlSimple and efficient modifications of well known techniques for reliable growth of high-quality crystals of small bioorganic moleculestext4472014-06-14Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767teaching and educationmed@iucr.org1600-5767A survey of the structural models proposed for PbZr1−xTixO3 using mode analysishttp://scripts.iucr.org/cgi-bin/paper?ks5424
The numerous structures that have been reported for the different phases of the lead zirconate titanate system, PbZr1−xTixO3 (PZT), are analysed by means of a systematic symmetry-mode analysis. The distortion corresponding to the order parameter has been separated out and expressed in all phases in a comparable form. The fact that the physical origin of the PZT phases is an unstable threefold degenerate polar mode, plus in some cases an unstable octahedral tilting mode, produces structural correlations between the different phases. These correlations had remained unnoticed until now but are directly observable in a mode parameterization. They can be used both to characterize the evolution of the order parameters through the phase diagram and as a stringent test of the reported structural models. It is further shown that the activity of a single polar mode yields a specific feature in the mode decomposition of the monoclinic phases. This single-mode signature can be observed in the majority of the monoclinic structures proposed, making the others questionable. In fact, this internal constraint is satisfied by PZT to such a high degree that it drastically reduces the number of effective structural degrees of freedom. It is conjectured that this type of structural constraint beyond space-group symmetry can be a rather general property of low-symmetry distorted structures. As shown here, its existence can be detected and assessed by a symmetry-mode analysis, if considered in relation to the single underlying multidimensional order parameter.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Kocsis, B.Perez-Mato, J.M.Tasci, E.S.Flor, G. de laAroyo, M.I.2014-06-25doi:10.1107/S1600576714010693International Union of CrystallographyMode analysis and comparison of reported different phases of lead zirconate titanate was carried out. Most of the structural models comply with expected single three-dimensional order parameter correlations.enLEAD ZIRCONATE TITANATE; SYMMETRY-MODE ANALYSIS; STRUCTURAL CORRELATIONS; MULTIPLE PHASESThe numerous structures that have been reported for the different phases of the lead zirconate titanate system, PbZr1−xTixO3 (PZT), are analysed by means of a systematic symmetry-mode analysis. The distortion corresponding to the order parameter has been separated out and expressed in all phases in a comparable form. The fact that the physical origin of the PZT phases is an unstable threefold degenerate polar mode, plus in some cases an unstable octahedral tilting mode, produces structural correlations between the different phases. These correlations had remained unnoticed until now but are directly observable in a mode parameterization. They can be used both to characterize the evolution of the order parameters through the phase diagram and as a stringent test of the reported structural models. It is further shown that the activity of a single polar mode yields a specific feature in the mode decomposition of the monoclinic phases. This single-mode signature can be observed in the majority of the monoclinic structures proposed, making the others questionable. In fact, this internal constraint is satisfied by PZT to such a high degree that it drastically reduces the number of effective structural degrees of freedom. It is conjectured that this type of structural constraint beyond space-group symmetry can be a rather general property of low-symmetry distorted structures. As shown here, its existence can be detected and assessed by a symmetry-mode analysis, if considered in relation to the single underlying multidimensional order parameter.text/htmlA survey of the structural models proposed for PbZr1−xTixO3 using mode analysistext4472014-06-25Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767feature articles1165med@iucr.org11791600-5767The α–β phase transition in volcanic cristobalitehttp://scripts.iucr.org/cgi-bin/paper?ks5415
Cristobalite is a common mineral in volcanic ash produced from dome-forming eruptions. Assessment of the respiratory hazard posed by volcanic ash requires understanding the nature of the cristobalite it contains. Volcanic cristobalite contains coupled substitutions of Al3+ and Na+ for Si4+; similar co-substitutions in synthetic cristobalite are known to modify the crystal structure, affecting the stability of the α and β forms and the observed transition between them. Here, for the first time, the dynamics and energy changes associated with the α–β phase transition in volcanic cristobalite are investigated using X-ray powder diffraction with simultaneous in situ heating and differential scanning calorimetry. At ambient temperature, volcanic cristobalite exists in the α form and has a larger cell volume than synthetic α-cristobalite; as a result, its diffraction pattern sits between ICDD α- and β-cristobalite library patterns, which could cause ambiguity in phase identification. On heating from ambient temperature, volcanic cristobalite exhibits a lower degree of thermal expansion than synthetic cristobalite, and it also has a lower α–β transition temperature (∼473 K) compared with synthetic cristobalite (upwards of 543 K); these observations are discussed in relation to the presence of Al3+ and Na+ defects. The transition shows a stable and reproducible hysteresis loop with α and β phases coexisting through the transition, suggesting that discrete crystals in the sample have different transition temperatures.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Damby, D.E.Llewellin, E.W.Horwell, C.J.Williamson, B.J.Najorka, J.Cressey, G.Carpenter, M.2014-06-14doi:10.1107/S160057671401070XInternational Union of CrystallographyVolcanic cristobalite commonly contains structural substitutions of Al3+ and Na+ for Si4+. Quantifying the effect of these substitutions on the crystal structure may provide insight into volcanic processes and the variable toxicity of crystalline silica.enCRISTOBALITE; PHASE TRANSITIONSCristobalite is a common mineral in volcanic ash produced from dome-forming eruptions. Assessment of the respiratory hazard posed by volcanic ash requires understanding the nature of the cristobalite it contains. Volcanic cristobalite contains coupled substitutions of Al3+ and Na+ for Si4+; similar co-substitutions in synthetic cristobalite are known to modify the crystal structure, affecting the stability of the α and β forms and the observed transition between them. Here, for the first time, the dynamics and energy changes associated with the α–β phase transition in volcanic cristobalite are investigated using X-ray powder diffraction with simultaneous in situ heating and differential scanning calorimetry. At ambient temperature, volcanic cristobalite exists in the α form and has a larger cell volume than synthetic α-cristobalite; as a result, its diffraction pattern sits between ICDD α- and β-cristobalite library patterns, which could cause ambiguity in phase identification. On heating from ambient temperature, volcanic cristobalite exhibits a lower degree of thermal expansion than synthetic cristobalite, and it also has a lower α–β transition temperature (∼473 K) compared with synthetic cristobalite (upwards of 543 K); these observations are discussed in relation to the presence of Al3+ and Na+ defects. The transition shows a stable and reproducible hysteresis loop with α and β phases coexisting through the transition, suggesting that discrete crystals in the sample have different transition temperatures.text/htmlThe α–β phase transition in volcanic cristobalitetext4472014-06-14Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papersmed@iucr.org1600-5767MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteinshttp://scripts.iucr.org/cgi-bin/paper?aj5230
Time-resolved small- and wide-angle X-ray scattering (SAXS and WAXS) methods probe the structural dynamics of proteins in solution. Although technologically advanced, these methods are in many cases limited by data interpretation. The calculation of X-ray scattering profiles is computationally demanding and poses a bottleneck for all SAXS/WAXS-assisted structural refinement and, in particular, for the analysis of time-resolved data. A way of speeding up these calculations is to represent biomolecules as collections of coarse-grained scatterers. Here, such coarse-graining schemes are presented and discussed and their accuracies examined. It is demonstrated that scattering factors coincident with the popular MARTINI coarse-graining scheme produce reliable difference scattering in the range 0 < q < 0.75 Å−1. The findings are promising for future attempts at X-ray scattering data analysis, and may help to bridge the gap between time-resolved experiments and their interpretation.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Niebling, S.Björling, A.Westenhoff, S.2014-06-14doi:10.1107/S1600576714009959International Union of CrystallographyForm factors for X-ray scattering calculations from coarse-grained MARTINI protein models are derived. The reliability at different levels of coarse-graining is evaluated and weighed against the gain in computational speed of the coarser models.enX-RAY SOLUTION SCATTERING; PROTEINS; COARSE-GRAINING; MARTINI; STRUCTURAL DYNAMICS; SMALL-ANGLE X-RAY SCATTERING (SAXS); WIDE-ANGLE X-RAY SCATTERING (WAXS); PROTEIN STRUCTURE REFINEMENTTime-resolved small- and wide-angle X-ray scattering (SAXS and WAXS) methods probe the structural dynamics of proteins in solution. Although technologically advanced, these methods are in many cases limited by data interpretation. The calculation of X-ray scattering profiles is computationally demanding and poses a bottleneck for all SAXS/WAXS-assisted structural refinement and, in particular, for the analysis of time-resolved data. A way of speeding up these calculations is to represent biomolecules as collections of coarse-grained scatterers. Here, such coarse-graining schemes are presented and discussed and their accuracies examined. It is demonstrated that scattering factors coincident with the popular MARTINI coarse-graining scheme produce reliable difference scattering in the range 0 < q < 0.75 Å−1. The findings are promising for future attempts at X-ray scattering data analysis, and may help to bridge the gap between time-resolved experiments and their interpretation.text/htmlMARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteinstext4472014-06-14Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papersmed@iucr.org1600-5767Towards a detailed resolution smearing kernel for time-of-flight neutron reflectometers. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?rg9037
In the paper by Nelson [J. Appl. Cryst. (2013), 46, 1338–1346], Charles Dewhurst is missing from the list of authors. The complete list of authors should be A. R. J. Nelson and C. D. Dewhurst.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Nelson, A.R.J.Dewhurst, C.D.2014-05-10doi:10.1107/S1600576714009595International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2013), 46, 1338–1346.enNEUTRON REFLECTOMETRY; TIME OF FLIGHT; RESOLUTIONIn the paper by Nelson [J. Appl. Cryst. (2013), 46, 1338–1346], Charles Dewhurst is missing from the list of authors. The complete list of authors should be A. R. J. Nelson and C. D. Dewhurst.text/htmlTowards a detailed resolution smearing kernel for time-of-flight neutron reflectometers. Corrigendumtext3472014-05-10Journal of Applied CrystallographyCopyright (c) 2014 International Union of Crystallography1600-5767addenda and errata1162med@iucr.org11621600-5767Using a commodity high-definition television for collaborative structural biologyhttp://scripts.iucr.org/cgi-bin/paper?po5002
Visualization of protein structures using stereoscopic systems is frequently needed by structural biologists working to understand a protein's structure–function relationships. Often several scientists are working as a team and need simultaneous interaction with each other and the graphics representations. Most existing molecular visualization tools support single-user tasks, which are not suitable for a collaborative group. Expensive caves, domes or geowalls have been developed, but the availability and low cost of high-definition televisions (HDTVs) and game controllers in the commodity entertainment market provide an economically attractive option to achieve a collaborative environment. This paper describes a low-cost environment, using standard consumer game controllers and commercially available stereoscopic HDTV monitors with appropriate signal converters for structural biology collaborations employing existing binary distributions of commonly used software packages like Coot, PyMOL, Chimera, VMD, O, Olex2 and others.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Yennamalli, R.Arangarasan, R.Bryden, A.Gleicher, M.Phillips, G.N. Jr2014-05-29doi:10.1107/S160057671400939XInternational Union of CrystallographyA method exploiting off-the-rack television and game controllers for use by crystallographers and their collaborators for enhanced experience of co-located discussions is presented.enCOLLABORATIVE STRUCTURAL BIOLOGY; PROTEIN STRUCTURE VISUALIZATIONVisualization of protein structures using stereoscopic systems is frequently needed by structural biologists working to understand a protein's structure–function relationships. Often several scientists are working as a team and need simultaneous interaction with each other and the graphics representations. Most existing molecular visualization tools support single-user tasks, which are not suitable for a collaborative group. Expensive caves, domes or geowalls have been developed, but the availability and low cost of high-definition televisions (HDTVs) and game controllers in the commodity entertainment market provide an economically attractive option to achieve a collaborative environment. This paper describes a low-cost environment, using standard consumer game controllers and commercially available stereoscopic HDTV monitors with appropriate signal converters for structural biology collaborations employing existing binary distributions of commonly used software packages like Coot, PyMOL, Chimera, VMD, O, Olex2 and others.text/htmlUsing a commodity high-definition television for collaborative structural biologytext3472014-05-29Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767laboratory notes1153med@iucr.org11571600-5767Magnetic field dependent small-angle neutron scattering on a Co nanorod array: evidence for intraparticle spin misalignmenthttp://scripts.iucr.org/cgi-bin/paper?he5651
The structural and magnetic properties of a cobalt nanorod array have been studied by means of magnetic field dependent small-angle neutron scattering (SANS). Measurement of the unpolarized SANS cross section dΣ/dΩ of the saturated sample in the two scattering geometries where the applied magnetic field H is either perpendicular or parallel to the wavevector ki of the incoming neutron beam allows one to separate nuclear from magnetic SANS, without employing the usual sector-averaging procedure. The analysis of the SANS data in the saturated state provides structural parameters (rod radius and centre-to-centre distance) that are in good agreement with results from electron microscopy. Between saturation and the coercive field, a strong field dependence of dΣ/dΩ is observed (in both geometries), which cannot be explained using the conventional expression of the magnetic SANS cross section of magnetic nanoparticles in a homogeneous nonmagnetic matrix. The origin of the strong field dependence of dΣ/dΩ is believed to be related to intradomain spin misalignment, due to magnetocrystalline and magnetoelastic anisotropies and magnetostatic stray fields.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Günther, A.Bick, J.-P.Szary, P.Honecker, D.Dewhurst, C.D.Keiderling, U.Feoktystov, A.V.Tschöpe, A.Birringer, R.Michels, A.2014-05-29doi:10.1107/S1600576714008413International Union of CrystallographyThe results of magnetic field dependent small-angle neutron scattering measurements on a cobalt nanorod array are reported. The data provide evidence for the existence of intraparticle spin disorder.enSMALL-ANGLE NEUTRON SCATTERING; MAGNETISM; MAGNETIC MATERIALS; NANORODSThe structural and magnetic properties of a cobalt nanorod array have been studied by means of magnetic field dependent small-angle neutron scattering (SANS). Measurement of the unpolarized SANS cross section dΣ/dΩ of the saturated sample in the two scattering geometries where the applied magnetic field H is either perpendicular or parallel to the wavevector ki of the incoming neutron beam allows one to separate nuclear from magnetic SANS, without employing the usual sector-averaging procedure. The analysis of the SANS data in the saturated state provides structural parameters (rod radius and centre-to-centre distance) that are in good agreement with results from electron microscopy. Between saturation and the coercive field, a strong field dependence of dΣ/dΩ is observed (in both geometries), which cannot be explained using the conventional expression of the magnetic SANS cross section of magnetic nanoparticles in a homogeneous nonmagnetic matrix. The origin of the strong field dependence of dΣ/dΩ is believed to be related to intradomain spin misalignment, due to magnetocrystalline and magnetoelastic anisotropies and magnetostatic stray fields.text/htmlMagnetic field dependent small-angle neutron scattering on a Co nanorod array: evidence for intraparticle spin misalignmenttext3472014-05-29Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers992med@iucr.org9981600-5767A suite of software for processing MicroED data of extremely small protein crystalshttp://scripts.iucr.org/cgi-bin/paper?nb5108
Electron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. MicroED patterns, which are collected in a transmission electron microscope, were initially not amenable to indexing and intensity extraction by standard software, which necessitated the development of a suite of programs for data processing. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination. This ad hoc solution has been modified for more general use to provide a means for processing MicroED data until the technique can be fully implemented into existing crystallographic software packages. The suite is written in Python and the source code is available under a GNU General Public License.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Iadanza, M.G.Gonen, T.2014-05-29doi:10.1107/S1600576714008073International Union of CrystallographyElectron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination.enELECTRON DIFFRACTION; STRUCTURE DETERMINATION; COMPUTER PROGRAMSElectron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. MicroED patterns, which are collected in a transmission electron microscope, were initially not amenable to indexing and intensity extraction by standard software, which necessitated the development of a suite of programs for data processing. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination. This ad hoc solution has been modified for more general use to provide a means for processing MicroED data until the technique can be fully implemented into existing crystallographic software packages. The suite is written in Python and the source code is available under a GNU General Public License.text/htmlA suite of software for processing MicroED data of extremely small protein crystalstext3472014-05-29Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1140med@iucr.org11451600-5767Cheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction datahttp://scripts.iucr.org/cgi-bin/paper?he5638
The emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Barty, A.Kirian, R.A.Maia, F.R.N.C.Hantke, M.Yoon, C.H.White, T.A.Chapman, H.2014-05-29doi:10.1107/S1600576714007626International Union of CrystallographyThe emerging technique of serial X-ray diffraction requires new software tools for the efficient analysis of large volumes of data. Event selection early in the analysis pipeline is highly advantageous. The described software for classifying, sorting and analysing events is freely available to the general community.enFREE-ELECTRON LASERS; SERIAL CRYSTALLOGRAPHY; SERIAL X-RAY DIFFRACTIONThe emerging technique of serial X-ray diffraction, in which diffraction data are collected from samples flowing across a pulsed X-ray source at repetition rates of 100 Hz or higher, has necessitated the development of new software in order to handle the large data volumes produced. Sorting of data according to different criteria and rapid filtering of events to retain only diffraction patterns of interest results in significant reductions in data volume, thereby simplifying subsequent data analysis and management tasks. Meanwhile the generation of reduced data in the form of virtual powder patterns, radial stacks, histograms and other meta data creates data set summaries for analysis and overall experiment evaluation. Rapid data reduction early in the analysis pipeline is proving to be an essential first step in serial imaging experiments, prompting the authors to make the tool described in this article available to the general community. Originally developed for experiments at X-ray free-electron lasers, the software is based on a modular facility-independent library to promote portability between different experiments and is available under version 3 or later of the GNU General Public License.text/htmlCheetah: software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction datatext3472014-05-29Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers1118med@iucr.org11311600-5767An improved method for calibrating time-of-flight Laue single-crystal neutron diffractometershttp://scripts.iucr.org/cgi-bin/paper?fs5069
A robust and comprehensive method for determining the orientation matrix of a single-crystal sample using the neutron Laue time-of-flight (TOF) technique is described. The new method enables the measurement of the unit-cell parameters with an uncertainty in the range 0.015–0.06%, depending upon the crystal symmetry and the number of reflections measured. The improved technique also facilitates the location and integration of weak reflections, which are often more difficult to discern amongst the increased background at higher energies. The technique uses a mathematical model of the relative positions of all the detector pixels of the instrument, together with a methodology that establishes a reproducible reference frame and a method for determining the parameters of the instrument detector model. Since all neutron TOF instruments require precise detector calibration for their effective use, it is possible that the method described here may be of use on other instruments where the detector calibration cannot be determined by other means.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Bull, C.L.Johnson, M.W.Hamidov, H.Komatsu, K.Guthrie, M.Gutmann, M.J.Loveday, J.S.Nelmes, R.J.2014-05-29doi:10.1107/S1600576714006657International Union of CrystallographyAn improved method of calibrating neutron time-of-flight single-crystal instruments is described. The calibration method has led to improved lattice parameter determination and ability of the orientation matrix to describe the reflection positions on the detector surface.enNEUTRON DIFFRACTION; NEUTRON INSTRUMENTS; TIME-OF-FLIGHT; CALIBRATIONA robust and comprehensive method for determining the orientation matrix of a single-crystal sample using the neutron Laue time-of-flight (TOF) technique is described. The new method enables the measurement of the unit-cell parameters with an uncertainty in the range 0.015–0.06%, depending upon the crystal symmetry and the number of reflections measured. The improved technique also facilitates the location and integration of weak reflections, which are often more difficult to discern amongst the increased background at higher energies. The technique uses a mathematical model of the relative positions of all the detector pixels of the instrument, together with a methodology that establishes a reproducible reference frame and a method for determining the parameters of the instrument detector model. Since all neutron TOF instruments require precise detector calibration for their effective use, it is possible that the method described here may be of use on other instruments where the detector calibration cannot be determined by other means.text/htmlAn improved method for calibrating time-of-flight Laue single-crystal neutron diffractometerstext3472014-05-29Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767research papers974med@iucr.org9831600-5767GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macro­molecules in solutionhttp://scripts.iucr.org/cgi-bin/paper?to5062
Many research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here is GENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parameters via physical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Spinozzi, F.Ferrero, C.Ortore, M.G.De Maria Antolinos, A.Mariani, P.2014-05-10doi:10.1107/S1600576714005147International Union of CrystallographyGENFIT is a new computer code featuring an advanced model-fitting capability to analyse small-angle X-ray and neutron scattering data of macromolecular systems. Batches of experimental curves can be simultaneously best fitted using common parameters issued from combinations of models and, if applicable, constrained by physical and/or phenomenological relations.enGENFIT; SMALL-ANGLE X-RAY SCATTERING; SMALL-ANGLE NEUTRON SCATTERING; MACROMOLECULESMany research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here is GENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parameters via physical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems.text/htmlGENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macro­molecules in solutiontext3472014-05-10Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk1600-5767computer programs1132med@iucr.org11391600-5767Introduction to the special issue for the 15th International Conference on Small-Angle Scattering (SAS2012)http://scripts.iucr.org/cgi-bin/paper?me0538
Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Gilbert, E.P.Allen, A.J.2014-01-30doi:10.1107/S1600576714001770International Union of CrystallographyJournal of Applied Crystallography is pleased to announce a virtual issue presenting articles based on some highlights of the 15th International Small-Angle Scattering Conference (SAS2012). This special issue collects together a series of articles originally published in the journal between October 2013 and February 2014.enEDITORIALtext/htmlIntroduction to the special issue for the 15th International Conference on Small-Angle Scattering (SAS2012)text471Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallography2014-01-301editorial1600-5767med@iucr.org31600-5767Radioactive waste limits in cement to avoid leaching outhttp://scripts.iucr.org/cgi-bin/paper?nb5107
Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Helliwell, J.R.2014-01-30doi:10.1107/S1600576714000223International Union of CrystallographyNuclear waste management is an important challenge. Small-angle neutron scattering, transmission electron microscopy and mercury intrusion porosimetry have been brought to bear on the level of waste incorporation in cement and its impact on its mesoscopic structure. These results lead to a recommended limit for waste incorporation to avoid leaching out of the waste, clearly an undesirable property.enSMALL-ANGLE NEUTRON SCATTERING; CHEMICAL WASTE IMMOBILIZATION; CEMENTtext/htmlRadioactive waste limits in cement to avoid leaching outtext471Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallography2014-01-304scientific commentaries1600-5767med@iucr.org51600-5767Fast pole figure acquisition using area detectors at the DiffAbs beamline – Synchrotron SOLEIL. Erratumhttp://scripts.iucr.org/cgi-bin/paper?rw9043
Errors in the article by Mocuta, Richard, Fouet, Stanescu, Barbier, Guichet, Thomas, Hustache, Zozulya & Thiaudière [J. Appl. Cryst. (2013), 46, 1842–1853] are corrected.Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Mocuta, C.Richard, M.-I.Fouet, J.Stanescu, S.Barbier, A.Guichet, C.Thomas, O.Hustache, S.Zozulya, A.V.Thiaudière, D.2013-12-07doi:10.1107/S1600576713032081International Union of CrystallographyErrors in the article by Mocuta, Richard, Fouet, Stanescu, Barbier, Guichet, Thomas, Hustache, Zozulya & Thiaudière [J. Appl. Cryst. (2013), 46, 1842–1853] are corrected.enTEXTURE; POLE FIGURES; X-RAY DIFFRACTION; SYNCHROTRON RADIATIONErrors in the article by Mocuta, Richard, Fouet, Stanescu, Barbier, Guichet, Thomas, Hustache, Zozulya & Thiaudière [J. Appl. Cryst. (2013), 46, 1842–1853] are corrected.text/htmlFast pole figure acquisition using area detectors at the DiffAbs beamline – Synchrotron SOLEIL. Erratumtext471Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallography2013-12-07addenda and errata1600-5767med@iucr.org1600-5767Development of a simultaneous measurement system for SAXS–WAXD and the thickness of coating films during film formation by solvent evaporationhttp://scripts.iucr.org/cgi-bin/paper?fs5052
A system for the simultaneous measurement of small-angle X-ray scattering and wide-angle X-ray diffraction (SAXS–WAXD) and the thickness of a coating film, obtained with an automatic coater, during film formation has been developed. The system was installed on beamline BL03XU at SPring-8. As model specimens, poly(methyl methacrylate)-b-poly(n-butyl acrylate)-b-poly(methyl methacrylate) (PMMA-b-PnBA-b-PMMA) triblock copolymers with different compositions were used to investigate the film formation process during solvent evaporation. First of all, the data correction methods were examined for the coating films during solvent evaporation. Since the scattering invariant was affected by the scattering volume and the absorption of X-rays by the solvent and the copolymer during drying, the scattering invariant should be corrected for the film width and the X-ray absorption of the sample. The polymer concentration was estimated from the thickness of the coating film during solvent evaporation, while the X-ray absorption was evaluated by using the X-ray linear absorption coefficients of the solvent and the copolymer. The results showed that the correction of the scattering invariant is crucial for an exact description of the film formation process during solvent evaporation.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Shimokita, K.Miyazaki, T.Ogawa, H.Yamamoto, K.2014-01-30doi:10.1107/S1600576713031774International Union of CrystallographyA new simultaneous measurement system for small-angle X-ray scattering and wide-angle X-ray diffraction (SAXS–WAXD) and the thickness of coating films, and a data correction method for the scattering invariant from SAXS during solvent evaporation, are presented. The correction was important when investigating the film formation mechanism on drying.enCOATING FILMS; SOLVENT EVAPORATION; TRIBLOCK COPOLYMERS; MICROPHASE SEPARATIONA system for the simultaneous measurement of small-angle X-ray scattering and wide-angle X-ray diffraction (SAXS–WAXD) and the thickness of a coating film, obtained with an automatic coater, during film formation has been developed. The system was installed on beamline BL03XU at SPring-8. As model specimens, poly(methyl methacrylate)-b-poly(n-butyl acrylate)-b-poly(methyl methacrylate) (PMMA-b-PnBA-b-PMMA) triblock copolymers with different compositions were used to investigate the film formation process during solvent evaporation. First of all, the data correction methods were examined for the coating films during solvent evaporation. Since the scattering invariant was affected by the scattering volume and the absorption of X-rays by the solvent and the copolymer during drying, the scattering invariant should be corrected for the film width and the X-ray absorption of the sample. The polymer concentration was estimated from the thickness of the coating film during solvent evaporation, while the X-ray absorption was evaluated by using the X-ray linear absorption coefficients of the solvent and the copolymer. The results showed that the correction of the scattering invariant is crucial for an exact description of the film formation process during solvent evaporation.text/htmlDevelopment of a simultaneous measurement system for SAXS–WAXD and the thickness of coating films during film formation by solvent evaporationtext471http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2014-01-30476laboratory notes1600-5767med@iucr.org4811600-5767Analytical description of the scattering of cellulose nanocrystals in tracheid wood cells. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?ks9222
In the paper by Ogurreck & Müller [J. Appl. Cryst. (2010), 43, 256–263], Helga Lichtenegger is missing from the list of authors. The complete list of authors should be M. Ogurreck, H. C. Lichtenegger and M. Müller.Copyright (c) 2013 International Union of Crystallographyurn:issn:0021-8898Ogurreck, M.Lichtenegger, H.C.Müller, M.2013-11-15doi:10.1107/S0021889813031087International Union of CrystallographyCorrigendum to J. Appl. Cryst. (2010), 43, 256–263.enX-RAY DIFFRACTION; TRACHEID; FIBER TEXTURE; CELLULOSEIn the paper by Ogurreck & Müller [J. Appl. Cryst. (2010), 43, 256–263], Helga Lichtenegger is missing from the list of authors. The complete list of authors should be M. Ogurreck, H. C. Lichtenegger and M. Müller.text/htmlAnalytical description of the scattering of cellulose nanocrystals in tracheid wood cells. Corrigendumtext466Copyright (c) 2013 International Union of CrystallographyJournal of Applied Crystallography2013-11-151907addenda and errata0021-8898med@iucr.org19071600-5767Global small-angle X-ray scattering data analysis for multilamellar vesicles: the evolution of the scattering density profile modelhttp://scripts.iucr.org/cgi-bin/paper?fs5056
The highly successful scattering density profile (SDP) model, used to jointly analyze small-angle X-ray and neutron scattering data from unilamellar vesicles, has been adapted for use with data from fully hydrated, liquid crystalline multilamellar vesicles (MLVs). Using a genetic algorithm, this new method is capable of providing high-resolution structural information, as well as determining bilayer elastic bending fluctuations from standalone X-ray data. Structural parameters such as bilayer thickness and area per lipid were determined for a series of saturated and unsaturated lipids, as well as binary mixtures with cholesterol. The results are in good agreement with previously reported SDP data, which used both neutron and X-ray data. The inclusion of deuterated and non-deuterated MLV neutron data in the analysis improved the lipid backbone information but did not improve, within experimental error, the structural data regarding bilayer thickness and area per lipid.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Heftberger, P.Kollmitzer, B.Heberle, F.A.Pan, J.Rappolt, M.Amenitsch, H.Kučerka, N.Katsaras, J.Pabst, G.2013-12-25doi:10.1107/S1600576713029798International Union of CrystallographyThe high-resolution scattering length density analysis method has been generalized from unilamellar to multilamellar lipid vesicles. The method may be applied to X-ray data only, or to a joint analysis of X-ray and neutron data, yielding an improved refinement of the lipid backbone position.enSMALL-ANGLE X-RAY SCATTERING; SCATTERING DENSITY PROFILE MODEL; GENETIC ALGORITHMS; LIQUID CRYSTALLINE MULTILAMELLAR VESICLESThe highly successful scattering density profile (SDP) model, used to jointly analyze small-angle X-ray and neutron scattering data from unilamellar vesicles, has been adapted for use with data from fully hydrated, liquid crystalline multilamellar vesicles (MLVs). Using a genetic algorithm, this new method is capable of providing high-resolution structural information, as well as determining bilayer elastic bending fluctuations from standalone X-ray data. Structural parameters such as bilayer thickness and area per lipid were determined for a series of saturated and unsaturated lipids, as well as binary mixtures with cholesterol. The results are in good agreement with previously reported SDP data, which used both neutron and X-ray data. The inclusion of deuterated and non-deuterated MLV neutron data in the analysis improved the lipid backbone information but did not improve, within experimental error, the structural data regarding bilayer thickness and area per lipid.text/htmlGlobal small-angle X-ray scattering data analysis for multilamellar vesicles: the evolution of the scattering density profile modeltext471http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-12-25173research papers1600-5767med@iucr.org1801600-5767Three-dimensional rotation electron diffraction: software RED for automated data collection and data processinghttp://scripts.iucr.org/cgi-bin/paper?nb5079
Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05–0.20°) are combined with goniometer tilts at a coarse step (2.0–3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Wan, W.Sun, J.Su, J.Hovmöller, S.Zou, X.2013-11-15doi:10.1107/S0021889813027714International Union of CrystallographyImplementation of the RED software package for automated collection and processing of rotation electron diffraction data is described.enROTATION ELECTRON DIFFRACTION; ELECTRON DIFFRACTION TOMOGRAPHY; THREE-DIMENSIONAL ELECTRON DIFFRACTION; STRUCTURE ANALYSIS; ELECTRON DIFFRACTION; COMPUTER PROGRAMSImplementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs: RED data collection and RED data processing. The RED data collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05–0.20°) are combined with goniometer tilts at a coarse step (2.0–3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. The RED data processing program processes three-dimensional ED data generated by the RED data collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimensions. Unit-cell parameters are determined from the positions of reflections in three-dimensional reciprocal space. All reflections are indexed, and finally a list with hkl indices and intensities is output. The data processing program also includes a visualizer to view and analyse three-dimensional reciprocal lattices reconstructed from the ED frames. Details of the implementation are described. Data collection and data processing with the software RED are demonstrated using a calcined zeolite sample, silicalite-1. The structure of the calcined silicalite-1, with 72 unique atoms, could be solved from the RED data by routine direct methods.text/htmlThree-dimensional rotation electron diffraction: software RED for automated data collection and data processingtext466http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-11-151863research papers0021-8898med@iucr.org18731600-5767Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS modulehttp://scripts.iucr.org/cgi-bin/paper?kk5149
Fibrinogen is a large heterogeneous aggregation/degradation-prone protein playing a central role in blood coagulation and associated pathologies, whose structure is not completely resolved. When a high-molecular-weight fraction was analyzed by size-exclusion high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS), several composite peaks were apparent and because of the stickiness of fibrinogen the analysis was complicated by severe capillary fouling. Novel SAS analysis tools developed as a part of the UltraScan Solution Modeler (US-SOMO; http://somo.uthscsa.edu/), an open-source suite of utilities with advanced graphical user interfaces whose initial goal was the hydrodynamic modeling of biomacromolecules, were implemented and applied to this problem. They include the correction of baseline drift due to the accumulation of material on the SAXS capillary walls, and the Gaussian decomposition of non-baseline-resolved HPLC-SAXS elution peaks. It was thus possible to resolve at least two species co-eluting under the fibrinogen main monomer peak, probably resulting from in-column degradation, and two others under an oligomers peak. The overall and cross-sectional radii of gyration, molecular mass and mass/length ratio of all species were determined using the manual or semi-automated procedures available within the US-SOMO SAS module. Differences between monomeric species and linear and sideways oligomers were thus identified and rationalized. This new US-SOMO version additionally contains several computational and graphical tools, implementing functionalities such as the mapping of residues contributing to particular regions of P(r), and an advanced module for the comparison of primary I(q) versus q data with model curves computed from atomic level structures or bead models. It should be of great help in multi-resolution studies involving hydrodynamics, solution scattering and crystallographic/NMR data.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Brookes, E.Pérez, J.Cardinali, B.Profumo, A.Vachette, P.Rocco, M.2013-11-15doi:10.1107/S0021889813027751International Union of CrystallographyThe usefulness of a new high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS) data analysis module within the multi-resolution modeling suite US-SOMO is illustrated with size-exclusion small-angle X-ray scattering (SE-SAXS) data of a crude bovine serum albumin sample. The module is then applied to the SE-SAXS study of a human plasma fibrinogen high-molecular-weight fraction presenting severe aggregation problems and a split non-symmetrical main elution peak probably resulting from in-column degradation.enSMALL-ANGLE SCATTERING; CHROMATOGRAPHY; HPLC-SAXS; MULTI-RESOLUTION MODELING; BOVINE SERUM ALBUMIN; FIBRINOGENFibrinogen is a large heterogeneous aggregation/degradation-prone protein playing a central role in blood coagulation and associated pathologies, whose structure is not completely resolved. When a high-molecular-weight fraction was analyzed by size-exclusion high-performance liquid chromatography/small-angle X-ray scattering (HPLC-SAXS), several composite peaks were apparent and because of the stickiness of fibrinogen the analysis was complicated by severe capillary fouling. Novel SAS analysis tools developed as a part of the UltraScan Solution Modeler (US-SOMO; http://somo.uthscsa.edu/), an open-source suite of utilities with advanced graphical user interfaces whose initial goal was the hydrodynamic modeling of biomacromolecules, were implemented and applied to this problem. They include the correction of baseline drift due to the accumulation of material on the SAXS capillary walls, and the Gaussian decomposition of non-baseline-resolved HPLC-SAXS elution peaks. It was thus possible to resolve at least two species co-eluting under the fibrinogen main monomer peak, probably resulting from in-column degradation, and two others under an oligomers peak. The overall and cross-sectional radii of gyration, molecular mass and mass/length ratio of all species were determined using the manual or semi-automated procedures available within the US-SOMO SAS module. Differences between monomeric species and linear and sideways oligomers were thus identified and rationalized. This new US-SOMO version additionally contains several computational and graphical tools, implementing functionalities such as the mapping of residues contributing to particular regions of P(r), and an advanced module for the comparison of primary I(q) versus q data with model curves computed from atomic level structures or bead models. It should be of great help in multi-resolution studies involving hydrodynamics, solution scattering and crystallographic/NMR data.text/htmlFibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS moduletext466http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-11-151823research papers0021-8898med@iucr.org18331600-5767Refinement of macromolecular structures against neutron data with SHELXL2013http://scripts.iucr.org/cgi-bin/paper?he5625
Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392–400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.http://creativecommons.org/licenses/by/2.0/ukurn:issn:1600-5767Gruene, T.Hahn, H.W.Luebben, A.V.Meilleur, F.Sheldrick, G.M.2013-12-07doi:10.1107/S1600576713027659International Union of CrystallographySHELXL2013 contains improvements over the previous versions that facilitate the refinement of macromolecular structures against neutron data. This article highlights several features of particular interest for this purpose and includes a list of restraints for H-atom refinement.enSINGLE-CRYSTAL NEUTRON DIFFRACTION; MACROMOLECULAR STRUCTURE REFINEMENT; HYDROGEN RESTRAINTS; SHELXL2013Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392–400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.text/htmlRefinement of macromolecular structures against neutron data with SHELXL2013text471http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-12-07computer programs1600-5767med@iucr.org1600-5767A compact high-resolution X-ray powder diffractometerhttp://scripts.iucr.org/cgi-bin/paper?rw5057
A new powder diffractometer operating in transmission mode is described. It can work as a rapid very compact instrument or as a high-resolution instrument, and the sample preparation is simplified. The incident beam optics create pure Cu Kα1 radiation, giving rise to peak widths of ∼0.1° in 2θ in compact form with a sample-to-detector minimum radius of 55 mm, reducing to peak widths of <0.05° in high-resolution mode by increasing the detector radius to 240 mm. The resolution of the diffractometer is shown to be governed by a complex mixture of angular divergence, sample size, diffraction effects and the dimensions of the detector pixels. The data can be collected instantaneously, which combined with trivial sample preparation and no sample alignment, makes it a suitable method for very rapid phase identification. As the detector is moved further from the sample, the angular step from the pixel dimension is reduced and the resolution improves significantly for very detailed studies, including structure determination and analysis of the microstructure. The advantage of this geometry is that the resolution of the diffractometer can be calculated precisely and the instrumental artefacts can be analysed easily without a sample present. The performance is demonstrated with LaB6 and paracetamol, and a critical appraisal of the uncertainties in the measurements is presented. The instantaneous data collection offers possibilities in dynamic experiments.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Fewster, P.F.Trout, D.R.D.2013-11-15doi:10.1107/S0021889813027313International Union of CrystallographyA new powder diffractometer operating in transmission mode is described. It can work as a rapid very compact instrument or as a high-resolution instrument, and the sample preparation is simplified.enHIGH-RESOLUTION POWDER DIFFACTION; TRANSMISSION GEOMETRY; MONOCHROMATIZATIONA new powder diffractometer operating in transmission mode is described. It can work as a rapid very compact instrument or as a high-resolution instrument, and the sample preparation is simplified. The incident beam optics create pure Cu Kα1 radiation, giving rise to peak widths of ∼0.1° in 2θ in compact form with a sample-to-detector minimum radius of 55 mm, reducing to peak widths of <0.05° in high-resolution mode by increasing the detector radius to 240 mm. The resolution of the diffractometer is shown to be governed by a complex mixture of angular divergence, sample size, diffraction effects and the dimensions of the detector pixels. The data can be collected instantaneously, which combined with trivial sample preparation and no sample alignment, makes it a suitable method for very rapid phase identification. As the detector is moved further from the sample, the angular step from the pixel dimension is reduced and the resolution improves significantly for very detailed studies, including structure determination and analysis of the microstructure. The advantage of this geometry is that the resolution of the diffractometer can be calculated precisely and the instrumental artefacts can be analysed easily without a sample present. The performance is demonstrated with LaB6 and paracetamol, and a critical appraisal of the uncertainties in the measurements is presented. The instantaneous data collection offers possibilities in dynamic experiments.text/htmlA compact high-resolution X-ray powder diffractometertext466http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-11-151626research papers0021-8898med@iucr.org16391600-5767The interpretation of polycrystalline coherent inelastic neutron scattering from aluminiumhttp://scripts.iucr.org/cgi-bin/paper?he5613
A new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the (Q, ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Roach, D.L.Ross, D.K.Gale, J.D.Taylor, J.W.2013-10-26doi:10.1107/S0021889813023728International Union of CrystallographyPresented here is a method by which Q-dependent dispersive dynamics may be measured (and used to generate a lattice dynamical model) for polycrystalline samples. This method is analogous to the measurement of dispersion curves for single-crystal samples.enPOLYCRYSTALLINE COHERENT INELASTIC NEUTRON SCATTERINGA new approach to the interpretation and analysis of coherent inelastic neutron scattering from polycrystals (poly-CINS) is presented. This article describes a simulation of the one-phonon coherent inelastic scattering from a lattice model of an arbitrary crystal system. The one-phonon component is characterized by sharp features, determined, for example, by boundaries of the (Q, ω) regions where one-phonon scattering is allowed. These features may be identified with the same features apparent in the measured total coherent inelastic cross section, the other components of which (multiphonon or multiple scattering) show no sharp features. The parameters of the model can then be relaxed to improve the fit between model and experiment. This method is of particular interest where no single crystals are available. To test the approach, the poly-CINS has been measured for polycrystalline aluminium using the MARI spectrometer (ISIS), because both lattice dynamical models and measured dispersion curves are available for this material. The models used include a simple Lennard-Jones model fitted to the elastic constants of this material plus a number of embedded atom method force fields. The agreement obtained suggests that the method demonstrated should be effective in developing models for other materials where single-crystal dispersion curves are not available.text/htmlThe interpretation of polycrystalline coherent inelastic neutron scattering from aluminiumtext466http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-10-261755research papers0021-8898med@iucr.org17701600-57672014 American Crystallographic Association Patterson Award to John HelliwellThis notice is a slightly modified version of an article that originally appeared in the Summer 2013 issue of ACA RefleXions.http://scripts.iucr.org/cgi-bin/paper?me0524
Copyright (c) 2013 International Union of Crystallographyurn:issn:0021-8898Pastore, C.2013-10-01doi:10.1107/S0021889813023285International Union of CrystallographyenACA PATTERSON AWARDtext/html2014 American Crystallographic Association Patterson Award to John HelliwellThis notice is a slightly modified version of an article that originally appeared in the Summer 2013 issue of ACA RefleXions.text465Copyright (c) 2013 International Union of CrystallographyJournal of Applied Crystallography2013-10-011529crystallographers0021-8898med@iucr.org15301600-5767Complete elliptical ring geometry provides energy and instrument calibration for synchrotron-based two-dimensional X-ray diffractionhttp://scripts.iucr.org/cgi-bin/paper?he5594
A complete calibration method to characterize a static planar two-dimensional detector for use in X-ray diffraction at an arbitrary wavelength is described. This method is based upon geometry describing the point of intersection between a cone's axis and its elliptical conic section. This point of intersection is neither the ellipse centre nor one of the ellipse focal points, but some other point which lies in between. The presented solution is closed form, algebraic and non-iterative in its application, and gives values for the X-ray beam energy, the sample-to-detector distance, the location of the beam centre on the detector surface and the detector tilt relative to the incident beam. Previous techniques have tended to require prior knowledge of either the X-ray beam energy or the sample-to-detector distance, whilst other techniques have been iterative. The new calibration procedure is performed by collecting diffraction data, in the form of diffraction rings from a powder standard, at known displacements of the detector along the beam path.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Hart, M.L.Drakopoulos, M.Reinhard, C.Connolley, T.2013-10-01doi:10.1107/S0021889813022437International Union of CrystallographyA complete method for calibrating a two-dimensional flat-panel detector for use in X-ray diffraction is described. The method provides both the beam energy and the sample-to-detector distance. The geometry for the intersection of a cone's axis and its elliptical conic section is also presented.enINSTRUMENT CALIBRATION; SYNCHROTRON RADIATION; X-RAY DIFFRACTIONA complete calibration method to characterize a static planar two-dimensional detector for use in X-ray diffraction at an arbitrary wavelength is described. This method is based upon geometry describing the point of intersection between a cone's axis and its elliptical conic section. This point of intersection is neither the ellipse centre nor one of the ellipse focal points, but some other point which lies in between. The presented solution is closed form, algebraic and non-iterative in its application, and gives values for the X-ray beam energy, the sample-to-detector distance, the location of the beam centre on the detector surface and the detector tilt relative to the incident beam. Previous techniques have tended to require prior knowledge of either the X-ray beam energy or the sample-to-detector distance, whilst other techniques have been iterative. The new calibration procedure is performed by collecting diffraction data, in the form of diffraction rings from a powder standard, at known displacements of the detector along the beam path.text/htmlComplete elliptical ring geometry provides energy and instrument calibration for synchrotron-based two-dimensional X-ray diffractiontext465http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-10-011249research papers0021-8898med@iucr.org12601600-5767A wide-angle X-ray fibre diffraction method for quantifying collagen orientation across large tissue areas: application to the human eyeball coathttp://scripts.iucr.org/cgi-bin/paper?fs5053
A quantitative map of collagen fibril orientation across the human eyeball coat, including both the cornea and the sclera, has been obtained using a combination of synchrotron wide-angle X-ray scattering (WAXS) and three-dimensional point mapping. A macromolecular crystallography beamline, in a custom-modified fibre diffraction setup, was used to record the 1.6 nm intermolecular equatorial reflection from fibrillar collagen at 0.5 mm spatial resolution across a flat-mounted human eyeball coat. Fibril orientation, derived as an average measure of the tissue thickness, was quantified by extraction of the azimuthal distribution of WAXS scatter intensity. Vector plots of preferential fibre orientation were remapped onto an idealized eyeball surface using a custom-built numerical algorithm, to obtain a three-dimensional representation of the collagen fibril architecture.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Pijanka, J.K.Abass, A.Sorensen, T.Elsheikh, A.Boote, C.2013-09-18doi:10.1107/S0021889813022358International Union of CrystallographyA wide-angle X-ray fibre diffraction method is presented, which allows quantification of collagen orientation across large tissue areas. Application to the human eyeball coat (cornea and sclera) has yielded detailed maps of preferred fibril orientation and isotropic collagen distribution.enHUMAN EYE; CORNEA; SCLERA; COLLAGEN; WIDE-ANGLE X-RAY FIBRE DIFFRACTIONA quantitative map of collagen fibril orientation across the human eyeball coat, including both the cornea and the sclera, has been obtained using a combination of synchrotron wide-angle X-ray scattering (WAXS) and three-dimensional point mapping. A macromolecular crystallography beamline, in a custom-modified fibre diffraction setup, was used to record the 1.6 nm intermolecular equatorial reflection from fibrillar collagen at 0.5 mm spatial resolution across a flat-mounted human eyeball coat. Fibril orientation, derived as an average measure of the tissue thickness, was quantified by extraction of the azimuthal distribution of WAXS scatter intensity. Vector plots of preferential fibre orientation were remapped onto an idealized eyeball surface using a custom-built numerical algorithm, to obtain a three-dimensional representation of the collagen fibril architecture.text/htmlA wide-angle X-ray fibre diffraction method for quantifying collagen orientation across large tissue areas: application to the human eyeball coattext465http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-09-181481research papers0021-8898med@iucr.org14891600-5767A novel small-angle neutron scattering detector geometry. Corrigendumhttp://scripts.iucr.org/cgi-bin/paper?he9597
Errors in the paper by Kanaki, Jackson, Hall-Wilton, Piscitelli, Kirstein & Andersen [J. Appl. Cryst. (2013), 46, 1031–1037] are corrected.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Kanaki, K.Jackson, A.Hall-Wilton, R.Piscitelli, F.Kirstein, O.Andersen, K.H.2013-10-01doi:10.1107/S0021889813022826International Union of CrystallographyErrors in the paper by Kanaki, Jackson, Hall-Wilton, Piscitelli, Kirstein & Andersen [J. Appl. Cryst. (2013), 46, 1031–1037] are corrected.enBORON-10; BORON CARBIDE; DETECTORS; EUROPEAN SPALLATION SOURCE (ESS); HELIUM-3; GEOMETRY; NEUTRONS; OPTIMIZATION BASED ON MATERIAL PROPERTIES; SMALL-ANGLE NEUTRON SCATTERING (SANS)Errors in the paper by Kanaki, Jackson, Hall-Wilton, Piscitelli, Kirstein & Andersen [J. Appl. Cryst. (2013), 46, 1031–1037] are corrected.text/htmlA novel small-angle neutron scattering detector geometry. Corrigendumtext465http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-10-011528addenda and errata0021-8898med@iucr.org15281600-5767X-ray analysis of residual stress gradients in TiN coatings by a Laplace space approach and cross-sectional nanodiffraction: a critical comparisonhttp://scripts.iucr.org/cgi-bin/paper?rw5051
Novel scanning synchrotron cross-sectional nanobeam and conventional laboratory as well as synchrotron Laplace X-ray diffraction methods are used to characterize residual stresses in exemplary 11.5 µm-thick TiN coatings. Both real and Laplace space approaches reveal a homogeneous tensile stress state and a very pronounced compressive stress gradient in as-deposited and blasted coatings, respectively. The unique capabilities of the cross-sectional approach operating with a beam size of 100 nm in diameter allow the analysis of stress variation with sub-micrometre resolution at arbitrary depths and the correlation of the stress evolution with the local coating microstructure. Finally, advantages and disadvantages of both approaches are extensively discussed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Stefenelli, M.Todt, J.Riedl, A.Ecker, W.Müller, T.Daniel, R.Burghammer, M.Keckes, J.2013-10-01doi:10.1107/S0021889813019535International Union of CrystallographyResidual stresses in as-deposited and blasted TiN coatings are characterized using a Laplace approach and using the novel cross-sectional X-ray nanodiffraction technique. A comparison of real and Laplace space techniques demonstrates the advantages of the nanodiffraction method, with a possibility to analyse local gradients of stress, texture, crystallite size and phase in thin films and coatings.enRESIDUAL STRESS; TIN COATINGS; LAPLACE METHODS; X-RAY DIFFRACTION; CROSS-SECTIONAL NANODIFFRACTIONNovel scanning synchrotron cross-sectional nanobeam and conventional laboratory as well as synchrotron Laplace X-ray diffraction methods are used to characterize residual stresses in exemplary 11.5 µm-thick TiN coatings. Both real and Laplace space approaches reveal a homogeneous tensile stress state and a very pronounced compressive stress gradient in as-deposited and blasted coatings, respectively. The unique capabilities of the cross-sectional approach operating with a beam size of 100 nm in diameter allow the analysis of stress variation with sub-micrometre resolution at arbitrary depths and the correlation of the stress evolution with the local coating microstructure. Finally, advantages and disadvantages of both approaches are extensively discussed.text/htmlX-ray analysis of residual stress gradients in TiN coatings by a Laplace space approach and cross-sectional nanodiffraction: a critical comparisontext465http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-10-011378research papers0021-8898med@iucr.org13851600-5767Strain distribution in an Si single crystal measured by interference fringes of X-ray mirage diffractionhttp://scripts.iucr.org/cgi-bin/paper?to5040
In X-ray interference fringes accompanied by mirage diffraction, variations have been observed in the spacing and position of the fringes from a plane-parallel Si single crystal fixed at one end as a function of distance from the incident plane of the X-rays to the free crystal end. The variations can be explained by distortion of the sample crystal due to gravity. From the variations and positions of the fringes, the strain gradient of the crystal has been determined. The distribution of the observed strain agrees with that expected from rod theory except for residual strain. When the distortion is large, the observed strain distribution does not agree with that expected from rod theory.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Jongsukswat, S.Fukamachi, T.Ju, D.Negishi, R.Hirano, K.Kawamura, T.2013-10-01doi:10.1107/S0021889813019067International Union of CrystallographyUsing the spacing and position of X-ray interference fringes accompanied by mirage diffraction, the strain distribution of a plane-parallel Si single crystal fixed at one end has been measured as a function of the distance l from the incident plane of the X-rays to the crystal edge. The measured strain gradients are proportional to l2, which agrees with rod theory.enMIRAGE FRINGES; INTERFERENCE FRINGES; STRAIN DISTRIBUTION; STRAIN GRADIENTS; DYNAMIC THEORY OF X-RAY DIFFRACTION; DISTORTED CRYSTALSIn X-ray interference fringes accompanied by mirage diffraction, variations have been observed in the spacing and position of the fringes from a plane-parallel Si single crystal fixed at one end as a function of distance from the incident plane of the X-rays to the free crystal end. The variations can be explained by distortion of the sample crystal due to gravity. From the variations and positions of the fringes, the strain gradient of the crystal has been determined. The distribution of the observed strain agrees with that expected from rod theory except for residual strain. When the distortion is large, the observed strain distribution does not agree with that expected from rod theory.text/htmlStrain distribution in an Si single crystal measured by interference fringes of X-ray mirage diffractiontext465http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-10-011261research papers0021-8898med@iucr.org12651600-5767Interactive visualization tools for the structural biologisthttp://scripts.iucr.org/cgi-bin/paper?rw5038
In structural biology, management of a large number of Protein Data Bank (PDB) files and raw X-ray diffraction images often presents a major organizational problem. Existing software packages that manipulate these file types were not designed for these kinds of file-management tasks. This is typically encountered when browsing through a folder of hundreds of X-ray images, with the aim of rapidly inspecting the diffraction quality of a data set. To solve this problem, a useful functionality of the Macintosh operating system (OSX) has been exploited that allows custom visualization plugins to be attached to certain file types. Software plugins have been developed for diffraction images and PDB files, which in many scenarios can save considerable time and effort. The direct visualization of diffraction images and PDB structures in the file browser can be used to identify key files of interest simply by scrolling through a list of files.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Porebski, B.T.Ho, B.K.Buckle, A.M.2013-10-01doi:10.1107/S0021889813017858International Union of CrystallographyTwo software plugins are presented for the Mac OSX operating system that allow rapid and convenient visualization of PDB files and X-ray diffraction images directly within the file browser, without the need for full-featured applications.enPDB VISUALIZATION; X-RAY DIFFRACTION IMAGES; DATA MANAGEMENTIn structural biology, management of a large number of Protein Data Bank (PDB) files and raw X-ray diffraction images often presents a major organizational problem. Existing software packages that manipulate these file types were not designed for these kinds of file-management tasks. This is typically encountered when browsing through a folder of hundreds of X-ray images, with the aim of rapidly inspecting the diffraction quality of a data set. To solve this problem, a useful functionality of the Macintosh operating system (OSX) has been exploited that allows custom visualization plugins to be attached to certain file types. Software plugins have been developed for diffraction images and PDB files, which in many scenarios can save considerable time and effort. The direct visualization of diffraction images and PDB structures in the file browser can be used to identify key files of interest simply by scrolling through a list of files.text/htmlInteractive visualization tools for the structural biologisttext465http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-10-01computer programs0021-8898med@iucr.org1600-5767xrayutilities: a versatile tool for reciprocal space conversion of scattering data recorded with linear and area detectorshttp://scripts.iucr.org/cgi-bin/paper?rg5038
General algorithms to convert scattering data of linear and area detectors recorded in various scattering geometries to reciprocal space coordinates are presented. These algorithms work for any goniometer configuration including popular four-circle, six-circle and kappa goniometers. The use of commonly employed approximations is avoided and therefore the algorithms work also for large detectors at small sample–detector distances. A recipe for determining the necessary detector parameters including mostly ignored misalignments is given. The algorithms are implemented in a freely available open-source package.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Kriegner, D.Wintersberger, E.Stangl, J.2013-08-01doi:10.1107/S0021889813017214International Union of CrystallographyAlgorithms for the reciprocal space conversion of linear and area detectors are implemented in an open-source Python package.enX-RAY SCATTERING; DATA ANALYSIS; RECIPROCAL SPACE; COMPUTER PROGRAMSGeneral algorithms to convert scattering data of linear and area detectors recorded in various scattering geometries to reciprocal space coordinates are presented. These algorithms work for any goniometer configuration including popular four-circle, six-circle and kappa goniometers. The use of commonly employed approximations is avoided and therefore the algorithms work also for large detectors at small sample–detector distances. A recipe for determining the necessary detector parameters including mostly ignored misalignments is given. The algorithms are implemented in a freely available open-source package.text/htmlxrayutilities: a versatile tool for reciprocal space conversion of scattering data recorded with linear and area detectorstext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1162med@iucr.org11701600-5767Validation of three-dimensional diffraction contrast tomography reconstructions by means of electron backscatter diffraction characterizationhttp://scripts.iucr.org/cgi-bin/paper?ks5358
Microstructure reconstructions resulting from diffraction contrast tomography data of polycrystalline bulk strontium titanate were reinvestigated by means of electron backscatter diffraction (EBSD) characterization. Corresponding two-dimensional grain maps from the two characterization methods were aligned and compared, focusing on the spatial resolution at the internal interfaces. The compared grain boundary networks show a remarkably good agreement both morphologically and in crystallographic orientation. Deviations are critically assessed and discussed in the context of diffraction data reconstruction and EBSD data collection techniques.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Syha, M.Trenkle, A.Lödermann, B.Graff, A.Ludwig, W.Weygand, D.Gumbsch, P.2013-08-01doi:10.1107/S002188981301580XInternational Union of CrystallographyCorresponding two-dimensional grain maps from the diffraction contrast tomography and electron backscatter diffraction characterization methods were aligned and compared, focusing on the spatial resolution at the internal interfaces. The compared grain boundary networks show a remarkably good agreement both morphologically and in crystallographic orientation.enMICROSTRUCTURE CHARACTERIZATION; DIFFRACTION CONTRAST TOMOGRAPHY; ELECTRON BACKSCATTER DIFFRACTIONMicrostructure reconstructions resulting from diffraction contrast tomography data of polycrystalline bulk strontium titanate were reinvestigated by means of electron backscatter diffraction (EBSD) characterization. Corresponding two-dimensional grain maps from the two characterization methods were aligned and compared, focusing on the spatial resolution at the internal interfaces. The compared grain boundary networks show a remarkably good agreement both morphologically and in crystallographic orientation. Deviations are critically assessed and discussed in the context of diffraction data reconstruction and EBSD data collection techniques.text/htmlValidation of three-dimensional diffraction contrast tomography reconstructions by means of electron backscatter diffraction characterizationtext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1145med@iucr.org11501600-5767Composition-dependent structure of polycrystalline magnetron-sputtered V–Al–C–N hard coatings studied by XRD, XPS, XANES and EXAFShttp://scripts.iucr.org/cgi-bin/paper?nb5051
V–Al–C–N hard coatings with high carbon content were deposited by reactive radio-frequency magnetron sputtering using an experimental combinatorial approach, deposition from a segmented sputter target. The composition-dependent coexisting phases within the coating were analysed using the complementary methods of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge spectroscopy (XANES) and extended X-ray absorption fine-structure spectroscopy (EXAFS). For the analysis of the X-ray absorption near-edge spectra, a new approach for evaluation of the pre-edge peak was developed, taking into account the self-absorption effects in thin films. Within the studied composition range, a mixed face-centred cubic (V,Al)(C,N) phase coexisting with a C–C-containing phase was observed. No indication of hexagonal (V,Al)(N,C) was found. The example of V–Al–C–N demonstrates how important a combination of complementary methods is for the detection of coexisting phases in complex multi-element coatings.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Krause, B.Darma, S.Kaufholz, M.Mangold, S.Doyle, S.Ulrich, S.Leiste, H.Stüber, M.Baumbach, T.2013-08-01doi:10.1107/S0021889813014477International Union of CrystallographyV–Al–C–N hard coatings with high carbon content were deposited by reactive radio-frequency magnetron sputtering from a segmented sputter target. The composition-dependent coexisting phases were analysed using the complementary methods of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge spectroscopy (XANES) and extended X-ray absorption fine-structure spectroscopy (EXAFS).enSPUTTER DEPOSITION; HARD COATINGS; METASTABLE PHASES; NITRIDES; CARBIDES; AMORPHOUS CARBON; X-RAY PHOTOELECTRON SPECTROSCOPY (XPS); X-RAY ABSORPTION NEAR-EDGE SPECTROSCOPY (XANES); EXTENDED X-RAY ABSORPTION FINE-STRUCTURE SPECTROSCOPY (EXAFS)V–Al–C–N hard coatings with high carbon content were deposited by reactive radio-frequency magnetron sputtering using an experimental combinatorial approach, deposition from a segmented sputter target. The composition-dependent coexisting phases within the coating were analysed using the complementary methods of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge spectroscopy (XANES) and extended X-ray absorption fine-structure spectroscopy (EXAFS). For the analysis of the X-ray absorption near-edge spectra, a new approach for evaluation of the pre-edge peak was developed, taking into account the self-absorption effects in thin films. Within the studied composition range, a mixed face-centred cubic (V,Al)(C,N) phase coexisting with a C–C-containing phase was observed. No indication of hexagonal (V,Al)(N,C) was found. The example of V–Al–C–N demonstrates how important a combination of complementary methods is for the detection of coexisting phases in complex multi-element coatings.text/htmlComposition-dependent structure of polycrystalline magnetron-sputtered V–Al–C–N hard coatings studied by XRD, XPS, XANES and EXAFStext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1064med@iucr.org10751600-5767Graphene: Carbon in Two Dimensions. By Mikhail I. Katsnelson. Cambridge University Press, 2012. Price (hardcover) GBP 45.00. ISBN-13: 9780521195409.http://scripts.iucr.org/cgi-bin/paper?pf0113
Copyright (c) 2013 International Union of Crystallographyurn:issn:0021-8898Paufler, P.2013-08-01doi:10.1107/S0021889813013381International Union of CrystallographyenBOOK REVIEWtext/htmlGraphene: Carbon in Two Dimensions. By Mikhail I. Katsnelson. Cambridge University Press, 2012. Price (hardcover) GBP 45.00. ISBN-13: 9780521195409.text4462013-08-01Journal of Applied CrystallographyCopyright (c) 2013 International Union of Crystallography0021-8898book reviews1240med@iucr.org12411600-5767Electron Crystallography. Electron Microscopy and Electron Diffraction. By Xiaodong Zou, Sven Hovmöller and Peter Oleynikov. Oxford University Press, 2011. Price (hardcover) GBP 52.50. ISBN-13: 978-0-19-958020-0.http://scripts.iucr.org/cgi-bin/paper?pf0115
Copyright (c) 2014 International Union of Crystallographyurn:issn:1600-5767Hadermann, J.2014-02-22doi:10.1107/S1600576714002726International Union of CrystallographyenBOOK REVIEWtext/htmlElectron Crystallography. Electron Microscopy and Electron Diffraction. By Xiaodong Zou, Sven Hovmöller and Peter Oleynikov. Oxford University Press, 2011. Price (hardcover) GBP 52.50. ISBN-13: 978-0-19-958020-0.text472Copyright (c) 2014 International Union of CrystallographyJournal of Applied Crystallography2014-02-22book reviews1600-5767med@iucr.org1600-5767Nonlinear continuum growth model of multiscale reliefs as applied to rigorous analysis of multilayer short-wave scattering intensity. I. Gratingshttp://scripts.iucr.org/cgi-bin/paper?xz5012
It is shown that taking into proper account certain terms in the nonlinear continuum equation of thin-film growth makes it applicable to the simulation of the surface of multilayer gratings with large boundary profile heights and/or gradient jumps. The proposed model describes smoothing and displacement of Mo/Si and Al/Zr boundaries of gratings grown on Si substrates with a blazed groove profile by magnetron sputtering and ion-beam deposition. Computer simulation of the growth of multilayer Mo/Si and Al/Zr gratings has been conducted. Absolute diffraction efficiencies of Mo/Si and Al/Zr gratings in the extreme UV range have been found within the framework of boundary integral equations applied to the calculated boundary profiles. It has been demonstrated that the integrated approach to the calculation of boundary profiles and of the intensity of short-wave scattering by multilayer gratings developed here opens up a way to perform studies comparable in accuracy to measurements with synchrotron radiation, at least for known materials and growth techniques.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Goray, L.Lubov, M.2013-08-01doi:10.1107/S0021889813012387International Union of CrystallographyThe nonlinear continuum equation of thin-film growth is applicable to simulate the surface of multilayer gratings with large boundary profile heights and/or gradient jumps. The integrated approach to the calculation of boundary profiles and the intensity of short-wave scattering by multilayer gratings is a way of performing studies comparable in accuracy to measurements with synchrotron radiation for known materials and growth techniques.enCONTINUUM GROWTH MODEL; BOUNDARY PROFILES; BOUNDARY INTEGRAL EQUATION METHOD; SCATTERING INTENSITY; DIFFRACTION GRATING EFFICIENCY; MULTILAYER RELIEF GRATINGS; SOFT-X-RAY AND EXTREME ULTRAVIOLET RANGEIt is shown that taking into proper account certain terms in the nonlinear continuum equation of thin-film growth makes it applicable to the simulation of the surface of multilayer gratings with large boundary profile heights and/or gradient jumps. The proposed model describes smoothing and displacement of Mo/Si and Al/Zr boundaries of gratings grown on Si substrates with a blazed groove profile by magnetron sputtering and ion-beam deposition. Computer simulation of the growth of multilayer Mo/Si and Al/Zr gratings has been conducted. Absolute diffraction efficiencies of Mo/Si and Al/Zr gratings in the extreme UV range have been found within the framework of boundary integral equations applied to the calculated boundary profiles. It has been demonstrated that the integrated approach to the calculation of boundary profiles and of the intensity of short-wave scattering by multilayer gratings developed here opens up a way to perform studies comparable in accuracy to measurements with synchrotron radiation, at least for known materials and growth techniques.text/htmlNonlinear continuum growth model of multiscale reliefs as applied to rigorous analysis of multilayer short-wave scattering intensity. I. Gratingstext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers926med@iucr.org9321600-5767A novel small-angle neutron scattering detector geometryhttp://scripts.iucr.org/cgi-bin/paper?he5597
A novel 2π detector geometry for small-angle neutron scattering (SANS) applications is presented and its theoretical performance evaluated. Such a novel geometry is ideally suited for a SANS instrument at the European Spallation Source (ESS). Motivated by the low availability and high price of 3He, the new concept utilizes gaseous detectors with 10B as the neutron converter. The shape of the detector is inspired by an optimization process based on the properties of the conversion material. Advantages over the detector geometry traditionally used on SANS instruments are discussed. The angular and time resolutions of the proposed detector concept are shown to satisfy the requirements of the particular SANS instrument.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Kanaki, K.Jackson, A.Hall-Wilton, R.Piscitelli, F.Kirstein, O.Andersen, K.H.2013-08-01doi:10.1107/S0021889813011862International Union of CrystallographyA novel 2π detector geometry for small-angle neutron scattering (SANS) applications is presented and its theoretical performance evaluated. The shape of the detector is inspired by an optimization process based on the properties of the conversion material. Advantages over the detector geometry traditionally used on SANS instruments are discussed.enBORON-10; BORON CARBIDE; DETECTORS; EUROPEAN SPALLATION SOURCE (ESS); HELIUM-3; GEOMETRY; NEUTRONS; OPTIMIZATION BASED ON MATERIAL PROPERTIES; SMALL-ANGLE NEUTRON SCATTERING (SANS)A novel 2π detector geometry for small-angle neutron scattering (SANS) applications is presented and its theoretical performance evaluated. Such a novel geometry is ideally suited for a SANS instrument at the European Spallation Source (ESS). Motivated by the low availability and high price of 3He, the new concept utilizes gaseous detectors with 10B as the neutron converter. The shape of the detector is inspired by an optimization process based on the properties of the conversion material. Advantages over the detector geometry traditionally used on SANS instruments are discussed. The angular and time resolutions of the proposed detector concept are shown to satisfy the requirements of the particular SANS instrument.text/htmlA novel small-angle neutron scattering detector geometrytext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1031med@iucr.org10371600-5767Three-wave X-ray diffraction in distorted epitaxial structureshttp://scripts.iucr.org/cgi-bin/paper?xz5010
Three-wave diffraction has been measured for a set of GaN, AlN, AlGaN and ZnO epitaxial layers grown on c-sapphire. A Renninger scan for the primary forbidden 0001 reflection was used. For each of the three-wave combinations, θ-scan curves were measured. The intensity and angular width of both ϕ- and θ-scan three-wave peaks were analyzed. The experimental data were used to determine properties of the multiple diffraction pattern in highly distorted layers. It is shown that the FWHM of θ scans is highly sensitive to the structural perfection and strongly depends on the type of three-wave combination. The narrowest peaks are observed for multiple combinations with the largest l index of the secondary hkl reflection. An influence of the type of the dislocation structure on the θ-scan broadening was revealed. These experimental facts are interpreted by considering the scanning geometry in the reciprocal space and taking into account the disc-shaped reciprocal-lattice points. The total integrated intensities of all the three-wave combinations were determined and their ratios were found to be in only a qualitative agreement with the theory. For AlGaN layers, the presence of the nonzero 0001 reflection was revealed, in contrast to AlN and GaN films.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Kyutt, R.Scheglov, M.2013-08-01doi:10.1107/S0021889813011709International Union of CrystallographyThree-wave diffraction has been experimentally studied for a set of III–nitride and ZnO epitaxial films differing in thickness and structural perfection. Properties of the multiple diffraction pattern in highly distorted layers are analyzed.enX-RAY DIFFRACTION; MULTIPLE DIFFRACTION; EPITAXIAL LAYERS; STRUCTURAL DEFECTS; WURTZITE STRUCTUREThree-wave diffraction has been measured for a set of GaN, AlN, AlGaN and ZnO epitaxial layers grown on c-sapphire. A Renninger scan for the primary forbidden 0001 reflection was used. For each of the three-wave combinations, θ-scan curves were measured. The intensity and angular width of both ϕ- and θ-scan three-wave peaks were analyzed. The experimental data were used to determine properties of the multiple diffraction pattern in highly distorted layers. It is shown that the FWHM of θ scans is highly sensitive to the structural perfection and strongly depends on the type of three-wave combination. The narrowest peaks are observed for multiple combinations with the largest l index of the secondary hkl reflection. An influence of the type of the dislocation structure on the θ-scan broadening was revealed. These experimental facts are interpreted by considering the scanning geometry in the reciprocal space and taking into account the disc-shaped reciprocal-lattice points. The total integrated intensities of all the three-wave combinations were determined and their ratios were found to be in only a qualitative agreement with the theory. For AlGaN layers, the presence of the nonzero 0001 reflection was revealed, in contrast to AlN and GaN films.text/htmlThree-wave X-ray diffraction in distorted epitaxial structurestext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers861med@iucr.org8671600-5767Modified statistical dynamical diffraction theory: analysis of model SiGe heterostructureshttp://scripts.iucr.org/cgi-bin/paper?xz5011
A modified version of the statistical dynamical diffraction theory (mSDDT) permits full-pattern fitting of high-resolution X-ray diffraction scans from thin-film systems across the entire range from fully dynamic to fully kinematic scattering. The mSDDT analysis has been applied to a set of model SiGe/Si thin-film samples in order to define the capabilities of this approach. For defect-free materials that diffract at the dynamic limit, mSDDT analyses return structural information that is consistent with commercial dynamical diffraction simulation software. As defect levels increase and the diffraction characteristics shift towards the kinematic limit, the mSDDT provides new insights into the structural characteristics of these materials.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Shreeman, P.K.Dunn, K.A.Novak, S.W.Matyi, R.J.2013-08-01doi:10.1107/S0021889813011308International Union of CrystallographyA modified version of the statistical dynamical diffraction theory has been applied to a set of model SiGe/Si thin-film samples in order to define the capabilities of this approach for returning structural information from defective semiconductor heterostructures.enSTATISTICAL DYNAMICAL DIFFRACTION THEORY; DEFECTIVE SEMICONDUCTOR HETEROSTRUCTURESA modified version of the statistical dynamical diffraction theory (mSDDT) permits full-pattern fitting of high-resolution X-ray diffraction scans from thin-film systems across the entire range from fully dynamic to fully kinematic scattering. The mSDDT analysis has been applied to a set of model SiGe/Si thin-film samples in order to define the capabilities of this approach. For defect-free materials that diffract at the dynamic limit, mSDDT analyses return structural information that is consistent with commercial dynamical diffraction simulation software. As defect levels increase and the diffraction characteristics shift towards the kinematic limit, the mSDDT provides new insights into the structural characteristics of these materials.text/htmlModified statistical dynamical diffraction theory: analysis of model SiGe heterostructurestext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers912med@iucr.org9181600-5767Alloy formation during molecular beam epitaxy growth of Si-doped InAs nanowires on GaAs[111]Bhttp://scripts.iucr.org/cgi-bin/paper?xz5006
Vertically aligned InAs nanowires (NWs) doped with Si were grown self-assisted by molecular beam epitaxy on GaAs[111]B substrates covered with a thin SiOx layer. Using out-of-plane X-ray diffraction, the influence of Si supply on the growth process and nanostructure formation was studied. It was found that the number of parasitic crystallites grown between the NWs increases with increasing Si flux. In addition, the formation of a Ga0.2In0.8As alloy was observed if the growth was performed on samples covered by a defective oxide layer. This alloy formation is observed within the crystallites and not within the nanowires. The Ga concentration is determined from the lattice mismatch of the crystallites relative to the InAs nanowires. No alloy formation is found for samples with faultless oxide layers.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Davydok, A.Rieger, T.Biermanns, A.Saqib, M.Grap, T.Lepsa, M.I.Pietsch, U.2013-08-01doi:10.1107/S0021889813010522International Union of CrystallographyAn investigation of the influence of Si supply on the molecular beam epitaxy growth process and morphology of InAs nanowires grown on GaAs[111]B substrates is presented.enSEMICONDUCTOR NANOWIRES; MOLECULAR BEAM EPITAXY (MBE) GROWTH; X-RAY DIFFRACTIONVertically aligned InAs nanowires (NWs) doped with Si were grown self-assisted by molecular beam epitaxy on GaAs[111]B substrates covered with a thin SiOx layer. Using out-of-plane X-ray diffraction, the influence of Si supply on the growth process and nanostructure formation was studied. It was found that the number of parasitic crystallites grown between the NWs increases with increasing Si flux. In addition, the formation of a Ga0.2In0.8As alloy was observed if the growth was performed on samples covered by a defective oxide layer. This alloy formation is observed within the crystallites and not within the nanowires. The Ga concentration is determined from the lattice mismatch of the crystallites relative to the InAs nanowires. No alloy formation is found for samples with faultless oxide layers.text/htmlAlloy formation during molecular beam epitaxy growth of Si-doped InAs nanowires on GaAs[111]Btext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers893med@iucr.org8971600-5767Characterization of SiGe thin films using a laboratory X-ray instrumenthttp://scripts.iucr.org/cgi-bin/paper?xz5002
The technique of reciprocal space mapping using X-rays is a recognized tool for the nondestructive characterization of epitaxial films. X-ray scattering from epitaxial Si0.4Ge0.6 films on Si(100) substrates using a laboratory X-ray source was investigated. It is shown that a laboratory source with a rotating anode makes it possible to investigate the material parameters of the super-thin 2–6 nm layers. For another set of partially relaxed layers, 50–200 nm thick, it is shown that from a high-resolution reciprocal space map, conditioned from diffuse scattering on dislocations, it is possible to determine quantitatively from the shape of a diffraction peak (possessing no thickness fringes) additional parameters such as misfit dislocation density and layer thickness as well as concentration and relaxation.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Ulyanenkova, T.Myronov, M.Benediktovitch, A.Mikhalychev, A.Halpin, J.Ulyanenkov, A.2013-08-01doi:10.1107/S0021889813010492International Union of CrystallographyThis article reports the characterization of thin SiGe/Si(100) epilayers using reciprocal space maps measured by a laboratory X-ray instrument and a high-resolution X-ray diffraction study of partially relaxed SiGe/Si thin films.enTHIN FILMS; HIGH-RESOLUTION RECIPROCAL SPACE MAPPING; PARTLY RELAXED EPITAXIAL FILMS; MISFIT DISLOCATIONThe technique of reciprocal space mapping using X-rays is a recognized tool for the nondestructive characterization of epitaxial films. X-ray scattering from epitaxial Si0.4Ge0.6 films on Si(100) substrates using a laboratory X-ray source was investigated. It is shown that a laboratory source with a rotating anode makes it possible to investigate the material parameters of the super-thin 2–6 nm layers. For another set of partially relaxed layers, 50–200 nm thick, it is shown that from a high-resolution reciprocal space map, conditioned from diffuse scattering on dislocations, it is possible to determine quantitatively from the shape of a diffraction peak (possessing no thickness fringes) additional parameters such as misfit dislocation density and layer thickness as well as concentration and relaxation.text/htmlCharacterization of SiGe thin films using a laboratory X-ray instrumenttext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers898med@iucr.org9021600-5767Defect structure transformation after thermal annealing in a surface layer of Zn-implanted Si(001) substrateshttp://scripts.iucr.org/cgi-bin/paper?xz5007
A combination of high-resolution X-ray diffractometry, Rutherford back scattering spectroscopy and secondary-ion mass spectrometry (SIMS) methods were used to characterize structural transformations of the damaged layer in Si(001) substrates heavily doped by Zn ions after a multistage thermal treatment. The shape of the SIMS profiles for Zn atoms correlates with the crystal structure of the damaged layer and depends on the presence of the following factors influencing the mobility of Zn atoms: (i) an amorphous/crystalline (a/c) interface, (ii) end-of-range defects, which are located slightly deeper than the a/c interface; (iii) a surface area enriched by Si vacancies; and (iv) the chemical interaction of Zn with Si atoms, which leads to the formation of Zn-containing phases in the surface layer.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Shcherbachev, K.Privezentsev, V.Kulikauskas, V.Zatekin, V.Saraykin, V.2013-08-01doi:10.1107/S0021889813010169International Union of CrystallographyA combination of high-resolution X-ray diffractometry, Rutherford back scattering spectroscopy and secondary-ion mass spectrometry (SIMS) allowed the influence of structural transformations in the damaged layer of Si(001) substrates, heavily doped by Zn ions with a Zn depth redistribution, after a multistage thermal treatment to be revealed. The shape of the Zn SIMS profiles correlates with the crystal structure of the layer and depends on the presence of factors influencing the mobility of Zn atoms.enX-RAY DIFFRACTION; ION IMPLANTATION; RADIATION-INDUCED DEFECTS; SILICONA combination of high-resolution X-ray diffractometry, Rutherford back scattering spectroscopy and secondary-ion mass spectrometry (SIMS) methods were used to characterize structural transformations of the damaged layer in Si(001) substrates heavily doped by Zn ions after a multistage thermal treatment. The shape of the SIMS profiles for Zn atoms correlates with the crystal structure of the damaged layer and depends on the presence of the following factors influencing the mobility of Zn atoms: (i) an amorphous/crystalline (a/c) interface, (ii) end-of-range defects, which are located slightly deeper than the a/c interface; (iii) a surface area enriched by Si vacancies; and (iv) the chemical interaction of Zn with Si atoms, which leads to the formation of Zn-containing phases in the surface layer.text/htmlDefect structure transformation after thermal annealing in a surface layer of Zn-implanted Si(001) substratestext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers882med@iucr.org8861600-5767A look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXShttp://scripts.iucr.org/cgi-bin/paper?xk5010
In this work epitaxial growth of cobalt on CaF2(111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Suturin, S.M.Fedorov, V.V.Korovin, A.M.Valkovskiy, G.A.Konnikov, S.G.Tabuchi, M.Sokolov, N.S.2013-08-01doi:10.1107/S0021889813008777International Union of CrystallographyThree-dimensional reciprocal space mapping by X-ray and electron diffraction [namely grazing-incidence X-ray diffraction (GIXD), reflection high-energy electron diffraction (RHEED) and grazing-incidence small-angle X-ray scattering (GISAXS)] was used to explore the internal structure and shape of differently oriented epitaxial Co/CaF2 facetted nanoparticles.enCOBALT-ON-FLUORITE NANOPARTICLES; GRAZING-INCIDENCE X-RAY DIFFRACTION (GIXD); REFLECTION HIGH-ENERGY ELECTRON DIFFRACTION (RHEED); GRAZING-INCIDENCE SMALL-ANGLE X-RAY SCATTERING (GISAXS); EPITAXIAL GROWTH; THREE-DIMENSIONAL RECIPROCAL SPACE MAPPINGIn this work epitaxial growth of cobalt on CaF2(111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles.text/htmlA look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXStext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers874med@iucr.org8811600-5767The current approach to initial crystallization screening of proteins is under-sampledhttp://scripts.iucr.org/cgi-bin/paper?he5578
Protein crystallization conditions that resulted in crystal structures published by scientists at the MRC Laboratory of Molecular Biology (MRC-LMB, Cambridge, UK) have been analysed. It was observed that the more often a crystallization reagent had been used to formulate the initial conditions, the more often it was found in the reported conditions that yielded diffraction quality crystals. The present analysis shows that, despite the broad variety of reagents, they have the same impact overall on the yield of crystal structures. More interestingly, the correlation implies that, although the initial crystallization screen may be considered very large, it is an under-sampled combinatorial approach.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Gorrec, F.2013-06-01doi:10.1107/S0021889813008030International Union of CrystallographyForty-seven main reagents included in a large set of macromolecular crystallization conditions are shown to have a similar impact overall on the yield of crystal structures. It is also shown that the conditions formulated with such reagents are under-sampled.enMACROMOLECULAR CRYSTALLIZATION; SCREEN FORMULATION; CRYSTALLIZATION REAGENTS; CRYSTAL STRUCTUREProtein crystallization conditions that resulted in crystal structures published by scientists at the MRC Laboratory of Molecular Biology (MRC-LMB, Cambridge, UK) have been analysed. It was observed that the more often a crystallization reagent had been used to formulate the initial conditions, the more often it was found in the reported conditions that yielded diffraction quality crystals. The present analysis shows that, despite the broad variety of reagents, they have the same impact overall on the yield of crystal structures. More interestingly, the correlation implies that, although the initial crystallization screen may be considered very large, it is an under-sampled combinatorial approach.text/htmlThe current approach to initial crystallization screening of proteins is under-sampledtext3462013-06-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898short communications795med@iucr.org7971600-5767CCL: an algorithm for the efficient comparison of clustershttp://scripts.iucr.org/cgi-bin/paper?db5110
The systematic comparison of the atomic structure of solids and clusters has become an important task in crystallography, chemistry, physics and materials science, in particular in the context of structure prediction and structure determination of nanomaterials. In this work, an efficient and robust algorithm for the comparison of cluster structures is presented, which is based on the mapping of the point patterns of the two clusters onto each other. This algorithm has been implemented as the module CCL in the structure visualization and analysis program KPLOT.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Hundt, R.Schön, J.C.Neelamraju, S.Zagorac, J.Jansen, M.2013-06-01doi:10.1107/S0021889813006894International Union of CrystallographyAn efficient and robust algorithm for the comparison of clusters is presented. Several illustrative example applications are given, including the screening of sets of clusters generated during global optimizations and Monte Carlo/molecular dymanics simulations, the identification of specific structure fragments inside large clusters, and the study of structure–substructure relations of periodic crystals.enCLUSTER STRUCTURES; STRUCTURE PREDICTION; STRUCTURE DETERMINATION; NANOMATERIALS; COMPUTER PROGRAMSThe systematic comparison of the atomic structure of solids and clusters has become an important task in crystallography, chemistry, physics and materials science, in particular in the context of structure prediction and structure determination of nanomaterials. In this work, an efficient and robust algorithm for the comparison of cluster structures is presented, which is based on the mapping of the point patterns of the two clusters onto each other. This algorithm has been implemented as the module CCL in the structure visualization and analysis program KPLOT.text/htmlCCL: an algorithm for the efficient comparison of clusterstext3462013-06-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papersmed@iucr.org1600-5767Development and applications of a new neutron single-crystal diffractometer based on a two-dimensional large-area curved position-sensitive detectorhttp://scripts.iucr.org/cgi-bin/paper?fs5036
A new single-crystal neutron diffractometer based on a large-area curved two-dimensional position-sensitive detector (C-2DPSD) has been developed. The diffractometer commissioning is almost complete, together with development of the measurement methodology and the raw data processing software package, the Reciprocal Analyzer, and the instrument is now ready to be launched for users. Position decoding of the C-2DPSD is via a delay-line readout method with an effective angular range of 110 × 54° in the horizontal and vertical directions, respectively, with a nominal radius of curvature of 530 mm. The diffractometer is equipped with a Ge(311) mosaic monochromator and two supermirror vacuum guide paths, one before and one after the monochromator position. The commissioning incorporates corrections and calibration of the instrument using an NaCl crystal, various applications such as crystallographic and magnetic structure measurements, a crystallinity check on large crystals, and a study on the composition or dopant content of a mixed crystal of (TmxYb1−x)Mn2O5. The installation of the diffractometer and the measurement method, the calibration procedure and results, the raw data treatment and visualization, and several applications using the large C-2DPSD-based diffractometer are reported.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Lee, C.-H.Noda, Y.Ishikawa, Y.Kim, S.A.Moon, M.Kimura, H.Watanabe, M.Dohi, Y.2013-06-01doi:10.1107/S002188981300681XInternational Union of CrystallographyA new reactor-based neutron single-crystal diffractometer was developed based on a large-area curved position-sensitive detector with a delay-line readout method. Its instrumentation details are presented, including diffractometer construction, measurement method, raw data treatment and calibration, and various applications for structural studies are given to exploit the strengths of the diffractometer.enSINGLE-CRYSTAL NEUTRON DIFFRACTION; NEUTRON DIFFRACTOMETERS; CURVED TWO-DIMENSIONAL POSITION-SENSITIVE DETECTORSA new single-crystal neutron diffractometer based on a large-area curved two-dimensional position-sensitive detector (C-2DPSD) has been developed. The diffractometer commissioning is almost complete, together with development of the measurement methodology and the raw data processing software package, the Reciprocal Analyzer, and the instrument is now ready to be launched for users. Position decoding of the C-2DPSD is via a delay-line readout method with an effective angular range of 110 × 54° in the horizontal and vertical directions, respectively, with a nominal radius of curvature of 530 mm. The diffractometer is equipped with a Ge(311) mosaic monochromator and two supermirror vacuum guide paths, one before and one after the monochromator position. The commissioning incorporates corrections and calibration of the instrument using an NaCl crystal, various applications such as crystallographic and magnetic structure measurements, a crystallinity check on large crystals, and a study on the composition or dopant content of a mixed crystal of (TmxYb1−x)Mn2O5. The installation of the diffractometer and the measurement method, the calibration procedure and results, the raw data treatment and visualization, and several applications using the large C-2DPSD-based diffractometer are reported.text/htmlDevelopment and applications of a new neutron single-crystal diffractometer based on a two-dimensional large-area curved position-sensitive detectortext3462013-06-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers697med@iucr.org7081600-5767Covariant description of X-ray diffraction from anisotropically relaxed epitaxial structureshttp://scripts.iucr.org/cgi-bin/paper?xk5001
A general theoretical approach to the description of epitaxial layers with essentially different cell parameters and in-plane relaxation anisotropy has been developed. A covariant description of relaxation in such structures has been introduced. An iteration method for evaluation of these parameters on the basis of the diffraction data set has been worked out together with error analysis and reliability checking. The validity of the presented theoretical approaches has been proved with a-ZnO on r-sapphire samples grown in the temperature range from 573 K up to 1073 K. A covariant description of relaxation anisotropy for these samples has been estimated with data measured for different directions of the diffraction plane relative to the sample surface.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Zhylik, A.Benediktovitch, A.Feranchuk, I.Inaba, K.Mikhalychev, A.Ulyanenkov, A.2013-08-01doi:10.1107/S0021889813006171International Union of CrystallographyA general theoretical approach to the description of epitaxial layers with essentially different cell parameters and in-plane relaxation anisotropy is presented.enEPITAXIAL LAYERS; RELAXATION PARAMETERS; HIGH-RESOLUTION X-RAY DIFFRACTION; THEORETICAL APPROACHA general theoretical approach to the description of epitaxial layers with essentially different cell parameters and in-plane relaxation anisotropy has been developed. A covariant description of relaxation in such structures has been introduced. An iteration method for evaluation of these parameters on the basis of the diffraction data set has been worked out together with error analysis and reliability checking. The validity of the presented theoretical approaches has been proved with a-ZnO on r-sapphire samples grown in the temperature range from 573 K up to 1073 K. A covariant description of relaxation anisotropy for these samples has been estimated with data measured for different directions of the diffraction plane relative to the sample surface.text/htmlCovariant description of X-ray diffraction from anisotropically relaxed epitaxial structurestext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers919med@iucr.org9251600-5767Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRFhttp://scripts.iucr.org/cgi-bin/paper?he5588
The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Monaco, S.Gordon, E.Bowler, M.W.Delagenière, S.Guijarro, M.Spruce, D.Svensson, O.McSweeney, S.M.McCarthy, A.A.Leonard, G.Nanao, M.H.2013-06-01doi:10.1107/S0021889813006195International Union of CrystallographyA system for the automatic reduction of single and multi-position macromolecular crystallography data is presented.enAUTOMATION; DATA PROCESSING; MACROMOLECULAR CRYSTALLOGRAPHY; COMPUTER PROGRAMSThe development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.text/htmlAutomatic processing of macromolecular crystallography X-ray diffraction data at the ESRFtext3462013-06-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898computer programs804med@iucr.org8101600-5767Potential use of V-channel Ge(220) monochromators in X-ray metrology and imaginghttp://scripts.iucr.org/cgi-bin/paper?xk5006
While channel-cut crystals, in which the diffracting surfaces in an asymmetric cut are kept parallel, can provide beam collimation and spectral beam shaping, they can in addition provide beam compression or expansion if the cut is V-shaped. The compression/expansion ratio depends in this case on the total asymmetry factor. If the Ge(220) diffraction planes and a total asymmetry factor in excess of 10 are used, the rocking curves of two diffractors will have a sufficient overlap only if the second diffractor is tuned slightly with respect to the first one. This study compares and analyses several ways of overcoming this mismatch, which is due to refraction, when the Cu Kα1 beam is compressed 21-fold in a V21 monochromator. A more than sixfold intensity increase was obtained if the matching was improved either by a compositional variation or by a thermal deformation. This provided an intensity gain compared with the use of a simple slit in a symmetrical channel-cut monochromator. The first attempt to overcome the mismatch by introducing different types of X-ray prisms for the required beam deflection is described as well. The performance of the V-shaped monochromators is demonstrated in two applications. A narrow collimated monochromatic beam obtained in the beam compressing mode was used for high-resolution grazing-incidence small-angle X-ray scattering measurements of a silicon sample with corrupted surface. In addition, a two-dimensional Bragg magnifier, based on two crossed V15 channel monochromators in beam expansion mode and tuned by means of unequal asymmetries, was successfully applied to high-resolution imaging of test structures in combination with a Medipix detector.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Korytár, D.Vagovič, P.Végsö, K.Šiffalovič, P.Dobročka, E.Jark, W.Áč, V.Zápražný, Z.Ferrari, C.Cecilia, A.Hamann, E.Mikulík, P.Baumbach, T.Fiederle, M.Jergel, M.2013-08-01doi:10.1107/S0021889813006122International Union of CrystallographySeveral ways of tuning a higher asymmetry factor (>10) in V-channel X-ray monochromators, for metrological and imaging applications, were analysed. A more than sixfold intensity increase for compositionally and thermally tuned cases was achieved.enMETROLOGY; MONTEL OPTICS; BRAGG MAGNIFIER; CHANNEL-CUT CRYSTALWhile channel-cut crystals, in which the diffracting surfaces in an asymmetric cut are kept parallel, can provide beam collimation and spectral beam shaping, they can in addition provide beam compression or expansion if the cut is V-shaped. The compression/expansion ratio depends in this case on the total asymmetry factor. If the Ge(220) diffraction planes and a total asymmetry factor in excess of 10 are used, the rocking curves of two diffractors will have a sufficient overlap only if the second diffractor is tuned slightly with respect to the first one. This study compares and analyses several ways of overcoming this mismatch, which is due to refraction, when the Cu Kα1 beam is compressed 21-fold in a V21 monochromator. A more than sixfold intensity increase was obtained if the matching was improved either by a compositional variation or by a thermal deformation. This provided an intensity gain compared with the use of a simple slit in a symmetrical channel-cut monochromator. The first attempt to overcome the mismatch by introducing different types of X-ray prisms for the required beam deflection is described as well. The performance of the V-shaped monochromators is demonstrated in two applications. A narrow collimated monochromatic beam obtained in the beam compressing mode was used for high-resolution grazing-incidence small-angle X-ray scattering measurements of a silicon sample with corrupted surface. In addition, a two-dimensional Bragg magnifier, based on two crossed V15 channel monochromators in beam expansion mode and tuned by means of unequal asymmetries, was successfully applied to high-resolution imaging of test structures in combination with a Medipix detector.text/htmlPotential use of V-channel Ge(220) monochromators in X-ray metrology and imagingtext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers945med@iucr.org9521600-5767Dose optimization approach to fast X-ray microtomography of the lung alveolihttp://scripts.iucr.org/cgi-bin/paper?xk5008
A basic prerequisite for in vivo X-ray imaging of the lung is the exact determination of radiation dose. Achieving resolutions of the order of micrometres may become particularly challenging owing to increased dose, which in the worst case can be lethal for the imaged animal model. A framework for linking image quality to radiation dose in order to optimize experimental parameters in respect of dose reduction is presented. The approach may find application for current and future in vivo studies to facilitate proper experiment planning and radiation risk assessment on the one hand and exploit imaging capabilities on the other.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Lovric, G.Barré, S.F.Schittny, J.C.Roth-Kleiner, M.Stampanoni, M.Mokso, R.2013-08-01doi:10.1107/S0021889813005591International Union of CrystallographyA framework for linking image quality to radiation dose in order to optimize experimental parameters in respect of dose reduction is presented. enDOSE OPTIMIZATION; RADIATION DOSE; X-RAY MICROTOMOGRAPHY; LUNG AVEOLIA basic prerequisite for in vivo X-ray imaging of the lung is the exact determination of radiation dose. Achieving resolutions of the order of micrometres may become particularly challenging owing to increased dose, which in the worst case can be lethal for the imaged animal model. A framework for linking image quality to radiation dose in order to optimize experimental parameters in respect of dose reduction is presented. The approach may find application for current and future in vivo studies to facilitate proper experiment planning and radiation risk assessment on the one hand and exploit imaging capabilities on the other.text/htmlDose optimization approach to fast X-ray microtomography of the lung alveolitext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers856med@iucr.org8601600-5767Processing of projections containing phase contrast in laboratory micro-computerized tomography imaginghttp://scripts.iucr.org/cgi-bin/paper?xk5002
Free-space-propagation-based imaging belongs to several techniques for achieving phase contrast in the hard X-ray range. The basic precondition is to use an X-ray beam with a high degree of coherence. Although the best sources of coherent X-rays are synchrotrons, spatially coherent X-rays emitted from a sufficiently small spot of laboratory microfocus or sub-microfocus sources allow the transfer of some of the modern imaging techniques from synchrotrons to laboratories. Spatially coherent X-rays traverse a sample leading to a phase shift. Beam deflection induced by the local change of refractive index may be expressed as a dark–bright contrast on the edges of the object in an X-ray projection. This phenomenon of edge enhancement leads to an increase in spatial resolution of X-ray projections but may also lead to unpleasant artefacts in computerized tomography unless phase and absorption contributions are separated. The possibilities of processing X-ray images of lightweight objects containing phase contrast using phase-retrieval methods in laboratory conditions are tested and the results obtained are presented. For this purpose, simulated and recorded X-ray projections taken from a laboratory imaging system with a microfocus X-ray source and a high-resolution CCD camera were processed and a qualitative comparison of results was made.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Zápražný, Z.Korytár, D.Mikulík, P.Áč, V.2013-08-01doi:10.1107/S002188981300558XInternational Union of CrystallographyProcessing of phase-contrast images in laboratory conditions is described.enPHASE-CONTRAST IMAGING; X-RAY IMAGING; X-RAY RADIOGRAPHY; DIGITAL RADIOGRAPHY; COMPUTERIZED TOMOGRAPHY; COMPUTED RADIOGRAPHYFree-space-propagation-based imaging belongs to several techniques for achieving phase contrast in the hard X-ray range. The basic precondition is to use an X-ray beam with a high degree of coherence. Although the best sources of coherent X-rays are synchrotrons, spatially coherent X-rays emitted from a sufficiently small spot of laboratory microfocus or sub-microfocus sources allow the transfer of some of the modern imaging techniques from synchrotrons to laboratories. Spatially coherent X-rays traverse a sample leading to a phase shift. Beam deflection induced by the local change of refractive index may be expressed as a dark–bright contrast on the edges of the object in an X-ray projection. This phenomenon of edge enhancement leads to an increase in spatial resolution of X-ray projections but may also lead to unpleasant artefacts in computerized tomography unless phase and absorption contributions are separated. The possibilities of processing X-ray images of lightweight objects containing phase contrast using phase-retrieval methods in laboratory conditions are tested and the results obtained are presented. For this purpose, simulated and recorded X-ray projections taken from a laboratory imaging system with a microfocus X-ray source and a high-resolution CCD camera were processed and a qualitative comparison of results was made.text/htmlProcessing of projections containing phase contrast in laboratory micro-computerized tomography imagingtext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers933med@iucr.org9381600-5767Enhancement of field-effect mobility due to structural ordering in poly(3-hexylthiophene) films by the dip-coating techniquehttp://scripts.iucr.org/cgi-bin/paper?xk5004
Organic field-effect transistors (OFETs) were fabricated by depositing a regioregular poly(3-hexylthiophene) (P3HT) active layer using a dip-coating method. The field-effect mobility in OFETs depends on chain orientation and crystallinity and is related to direction and withdrawal speed with respect to the source/drain orientation. In this paper, how to control the structural and transport properties of P3HT films by coating parallel and perpendicular to the dipping direction is demonstrated. X-ray diffraction curves taken in the perpendicular direction exhibit a higher degree of crystalline ordering and edge-on conformation compared with those in the parallel direction; this finding correlates with the directional anisotropy of the OFET mobility. Both structural anisotropy and transport properties are enhanced upon thermal treatment.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Ali, K.Pietsch, U.Grigorian, S.2013-08-01doi:10.1107/S0021889813004718International Union of CrystallographyDip coating is a facile technique to control structure and electrical performance. Both structural anisotropy and transport properties are enhanced upon thermal treatment.enSTRUCTURAL ANISOTROPY; ELECTRICAL ANISOTROPY; GRAZING-INCIDENCE X-RAY DIFFRACTIONOrganic field-effect transistors (OFETs) were fabricated by depositing a regioregular poly(3-hexylthiophene) (P3HT) active layer using a dip-coating method. The field-effect mobility in OFETs depends on chain orientation and crystallinity and is related to direction and withdrawal speed with respect to the source/drain orientation. In this paper, how to control the structural and transport properties of P3HT films by coating parallel and perpendicular to the dipping direction is demonstrated. X-ray diffraction curves taken in the perpendicular direction exhibit a higher degree of crystalline ordering and edge-on conformation compared with those in the parallel direction; this finding correlates with the directional anisotropy of the OFET mobility. Both structural anisotropy and transport properties are enhanced upon thermal treatment.text/htmlEnhancement of field-effect mobility due to structural ordering in poly(3-hexylthiophene) films by the dip-coating techniquetext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers908med@iucr.org9111600-5767Three-dimensional rocking curve imaging to measure the effective distortion in the neighbourhood of a defect within a crystal: an ice examplehttp://scripts.iucr.org/cgi-bin/paper?xk5009
Rocking curve imaging (RCI) is a quantitative version of monochromatic beam diffraction topography that involves using a two-dimensional detector, each pixel of which records its own `local' rocking curve. From these local rocking curves one can reconstruct maps of particularly relevant quantities (e.g. integrated intensity, angular position of the centre of gravity, FWHM). Up to now RCI images have been exploited in the reflection case, giving a quantitative picture of the features present in a several-micrometre-thick subsurface layer. Recently, a three-dimensional Bragg diffraction imaging technique, which combines RCI with `pinhole' and `section' diffraction topography in the transmission case, was implemented. It allows three-dimensional images of defects to be obtained and measurement of three-dimensional distortions within a 50 × 50 × 50 µm elementary volume inside the crystal with angular misorientations down to 10−5–10−6 rad. In the present paper, this three-dimensional-RCI (3D-RCI) technique is used to study one of the grains of a three-grained ice polycrystal. The inception of the deformation process is followed by reconstructing virtual slices in the crystal bulk. 3D-RCI capabilities allow the effective distortion in the bulk of the crystal to be investigated, and the predictions of diffraction theories to be checked, well beyond what has been possible up to now.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Philip, A.Meyssonnier, J.Kluender, R.T.Baruchel, J.2013-08-01doi:10.1107/S002188981300472XInternational Union of CrystallographyA three-dimensional Bragg diffraction imaging technique, which combines rocking curve imaging with `pinhole' and `section' diffraction topography in the transmission case, allows three-dimensional lattice distortion in the bulk of an ice crystal under compression to be measured.enROCKING CURVE IMAGING (RCI); 3D-RCI; ICE CRYSTALS; CRYSTAL DISTORTION; CRYSTAL DEFECTSRocking curve imaging (RCI) is a quantitative version of monochromatic beam diffraction topography that involves using a two-dimensional detector, each pixel of which records its own `local' rocking curve. From these local rocking curves one can reconstruct maps of particularly relevant quantities (e.g. integrated intensity, angular position of the centre of gravity, FWHM). Up to now RCI images have been exploited in the reflection case, giving a quantitative picture of the features present in a several-micrometre-thick subsurface layer. Recently, a three-dimensional Bragg diffraction imaging technique, which combines RCI with `pinhole' and `section' diffraction topography in the transmission case, was implemented. It allows three-dimensional images of defects to be obtained and measurement of three-dimensional distortions within a 50 × 50 × 50 µm elementary volume inside the crystal with angular misorientations down to 10−5–10−6 rad. In the present paper, this three-dimensional-RCI (3D-RCI) technique is used to study one of the grains of a three-grained ice polycrystal. The inception of the deformation process is followed by reconstructing virtual slices in the crystal bulk. 3D-RCI capabilities allow the effective distortion in the bulk of the crystal to be investigated, and the predictions of diffraction theories to be checked, well beyond what has been possible up to now.text/htmlThree-dimensional rocking curve imaging to measure the effective distortion in the neighbourhood of a defect within a crystal: an ice exampletext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers842med@iucr.org8481600-5767High-quality quartz single crystals for high-energy-resolution inelastic X-ray scattering analyzershttp://scripts.iucr.org/cgi-bin/paper?xk5003
Spherical analyzers are well known instruments for inelastic X-ray scattering (IXS) experiments. High-resolution IXS experiments almost always use Si single crystals as monochromators and spherical analyzers. At higher energies (>20 keV) Si shows a high energy resolution (<10 meV), at an exact symmetric back-diffraction condition, since the energy resolution is given by the real part of the susceptibility or polarizability. However, at low energies (<10 keV), high energy resolution is difficult to achieve with Si. α-SiO2 (quartz) can be an option, since it offers high energy resolution at low energies. In this work, the characterization of high-quality α-SiO2 is presented. Such characterization is made by high-resolution rocking curve, topography and lattice parameter mapping in different samples from a single block. X-ray optics with α-SiO2 for IXS at lower energies (from 2.5 to 12.6 keV) with medium to high energy resolution (from 90 to 11 meV) are proposed and theoretically exploited.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Hönnicke, M.G.Huang, X.Cusatis, C.Koditwuakku, C.N.Cai, Y.Q.2013-08-01doi:10.1107/S0021889813004731International Union of CrystallographyHigh quality quartz (α-SiO2) crystals are characterized and their use for inelastic X-ray scattering analyzers are presented and discussed.enX-RAY OPTICS; QUARTZ SINGLE CRYSTALS; SPHERICAL ANALYZERS; INELASTIC X-RAY SCATTERING ANALYZERSSpherical analyzers are well known instruments for inelastic X-ray scattering (IXS) experiments. High-resolution IXS experiments almost always use Si single crystals as monochromators and spherical analyzers. At higher energies (>20 keV) Si shows a high energy resolution (<10 meV), at an exact symmetric back-diffraction condition, since the energy resolution is given by the real part of the susceptibility or polarizability. However, at low energies (<10 keV), high energy resolution is difficult to achieve with Si. α-SiO2 (quartz) can be an option, since it offers high energy resolution at low energies. In this work, the characterization of high-quality α-SiO2 is presented. Such characterization is made by high-resolution rocking curve, topography and lattice parameter mapping in different samples from a single block. X-ray optics with α-SiO2 for IXS at lower energies (from 2.5 to 12.6 keV) with medium to high energy resolution (from 90 to 11 meV) are proposed and theoretically exploited.text/htmlHigh-quality quartz single crystals for high-energy-resolution inelastic X-ray scattering analyzerstext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers939med@iucr.org9441600-5767Grazing-incidence X-ray diffraction of single GaAs nanowires at locations defined by focused ion beamshttp://scripts.iucr.org/cgi-bin/paper?xz5008
Grazing-incidence X-ray diffraction measurements on single GaAs nanowires (NWs) grown on a (111)-oriented GaAs substrate by molecular beam epitaxy are reported. The positions of the NWs are intentionally determined by a direct implantation of Au with focused ion beams. This controlled arrangement in combination with a nanofocused X-ray beam allows the in-plane lattice parameter of single NWs to be probed, which is not possible for randomly grown NWs. Reciprocal space maps were collected at different heights along the NW to investigate the crystal structure. Simultaneously, substrate areas with different distances from the Au-implantation spots below the NWs were probed. Around the NWs, the data revealed a 0.4% decrease in the lattice spacing in the substrate compared with the expected unstrained value. This suggests the presence of a compressed region due to Au implantation.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Bussone, G.Schott, R.Biermanns, A.Davydok, A.Reuter, D.Carbone, G.Schülli, T.U.Wieck, A.D.Pietsch, U.2013-08-01doi:10.1107/S0021889813004226International Union of CrystallographyThe crystalline structure of single free-standing GaAs nanowires, grown by molecular beam epitaxy on a GaAs substrate at specific positions defined by focused ion beams, and the substrate regions close to the Au-implanted regions are investigated through grazing-incidence X-ray diffraction.enSEMICONDUCTOR NANOWIRES; GROWTH; GRAZING-INCIDENCE X-RAY DIFFRACTION; GAASGrazing-incidence X-ray diffraction measurements on single GaAs nanowires (NWs) grown on a (111)-oriented GaAs substrate by molecular beam epitaxy are reported. The positions of the NWs are intentionally determined by a direct implantation of Au with focused ion beams. This controlled arrangement in combination with a nanofocused X-ray beam allows the in-plane lattice parameter of single NWs to be probed, which is not possible for randomly grown NWs. Reciprocal space maps were collected at different heights along the NW to investigate the crystal structure. Simultaneously, substrate areas with different distances from the Au-implantation spots below the NWs were probed. Around the NWs, the data revealed a 0.4% decrease in the lattice spacing in the substrate compared with the expected unstrained value. This suggests the presence of a compressed region due to Au implantation.text/htmlGrazing-incidence X-ray diffraction of single GaAs nanowires at locations defined by focused ion beamstext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers887med@iucr.org8921600-5767X-ray diffraction microscopy: emerging imaging techniques for nondestructive analysis of crystalline materials from the millimetre down to the nanometre scalehttp://scripts.iucr.org/cgi-bin/paper?me0503
Copyright (c) 2013 International Union of Crystallographyurn:issn:0021-8898Borbély, A.Kaysser-Pyzalla, A.R.2013-03-14doi:10.1107/S0021889813004160International Union of CrystallographyIn anticipation of the International Year of Crystallography in 2014, Journal of Applied Crystallography presents a virtual issue on recent developments in X-ray diffraction microscopy. This issue is available at http://journals.iucr.org/special_issues/2013/imaging/.enX-RAY DIFFRACTION MICROSCOPY; COMPUTED TOMOGRAPHY; DIFFRACTION CONTRAST TOMOGRAPHY; COHERENT DIFFRACTION IMAGING; EDITORIALtext/htmlX-ray diffraction microscopy: emerging imaging techniques for nondestructive analysis of crystalline materials from the millimetre down to the nanometre scaletext2462013-03-14Journal of Applied CrystallographyCopyright (c) 2013 International Union of Crystallography0021-8898editorial295med@iucr.org2961600-5767High-resolution X-ray diffraction and imaginghttp://scripts.iucr.org/cgi-bin/paper?me0511
http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Fewster, P.F.Baidakova, M.V.Kyutt, R.2013-08-01doi:10.1107/S0021889813016415International Union of CrystallographyThis issue of Journal of Applied Crystallography includes some highlights of the 11th Biennial Conference on High-Resolution X-ray Diffraction and Imaging (XTOP), held in St Petersburg in 2012.enHIGH-RESOLUTION X-RAY DIFFRACTION; IMAGING; EDITORIALtext/htmlHigh-resolution X-ray diffraction and imagingtext464http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-08-01841editorial0021-8898med@iucr.org8411600-5767Crack propagation and fracture in silicon wafers under thermal stresshttp://scripts.iucr.org/cgi-bin/paper?xz5004
The behaviour of microcracks in silicon during thermal annealing has been studied using in situ X-ray diffraction imaging. Initial cracks are produced with an indenter at the edge of a conventional Si wafer, which was heated under temperature gradients to produce thermal stress. At temperatures where Si is still in the brittle regime, the strain may accumulate if a microcrack is pinned. If a critical value is exceeded either a new or a longer crack will be formed, which results with high probability in wafer breakage. The strain reduces most efficiently by forming (hhl) or (hkl) crack planes of high energy instead of the expected low-energy cleavage planes like {111}. Dangerous cracks, which become active during heat treatment and may shatter the whole wafer, can be identified from diffraction images simply by measuring the geometrical dimensions of the strain-related contrast around the crack tip. Once the plastic regime at higher temperature is reached, strain is reduced by generating dislocation loops and slip bands and no wafer breakage occurs. There is only a small temperature window within which crack propagation is possible during rapid annealing.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Danilewsky, A.Wittge, J.Kiefl, K.Allen, D.McNally, P.Garagorri, J.Elizalde, M.R.Baumbach, T.Tanner, B.K.2013-08-01doi:10.1107/S0021889813003695International Union of CrystallographyThe microcrack propagation and cleavage behaviour in silicon wafers during thermal annealing has been studied by in situ X-ray diffraction imaging (topography).enMICROCRACKS; SILICON WAFER FRACTURE; IN SITU OBSERVATIONS; X-RAY DIFFRACTION IMAGINGThe behaviour of microcracks in silicon during thermal annealing has been studied using in situ X-ray diffraction imaging. Initial cracks are produced with an indenter at the edge of a conventional Si wafer, which was heated under temperature gradients to produce thermal stress. At temperatures where Si is still in the brittle regime, the strain may accumulate if a microcrack is pinned. If a critical value is exceeded either a new or a longer crack will be formed, which results with high probability in wafer breakage. The strain reduces most efficiently by forming (hhl) or (hkl) crack planes of high energy instead of the expected low-energy cleavage planes like {111}. Dangerous cracks, which become active during heat treatment and may shatter the whole wafer, can be identified from diffraction images simply by measuring the geometrical dimensions of the strain-related contrast around the crack tip. Once the plastic regime at higher temperature is reached, strain is reduced by generating dislocation loops and slip bands and no wafer breakage occurs. There is only a small temperature window within which crack propagation is possible during rapid annealing.text/htmlCrack propagation and fracture in silicon wafers under thermal stresstext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers849med@iucr.org8551600-5767In situ X-ray crystallographic study of the structural evolution of colloidal crystals upon heatinghttp://scripts.iucr.org/cgi-bin/paper?xz5005
The structural evolution of colloidal crystals made of polystyrene hard spheres has been studied in situ upon incremental heating of a crystal in a temperature range below and above the glass transition temperature of polystyrene. Thin films of colloidal crystals having different particle sizes were studied in transmission geometry using a high-resolution small-angle X-ray scattering setup at the P10 Coherence Beamline of the PETRA III synchrotron facility. The transformation of colloidal crystals to a melted state has been observed in a narrow temperature interval of less than 10 K.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Zozulya, A.V.Meijer, J.-M.Shabalin, A.Ricci, A.Westermeier, F.Kurta, R.P.Lorenz, U.Singer, A.Yefanov, O.Petukhov, A.V.Sprung, M.Vartanyants, I.A.2013-08-01doi:10.1107/S0021889813003725International Union of CrystallographyThe results of a real-time X-ray crystallographic study of the melting transition of polystyrene colloidal crystals during heating are presented.enCOLLOIDAL CRYSTALS; SMALL-ANGLE X-RAY SCATTERING; THERMAL TREATMENTThe structural evolution of colloidal crystals made of polystyrene hard spheres has been studied in situ upon incremental heating of a crystal in a temperature range below and above the glass transition temperature of polystyrene. Thin films of colloidal crystals having different particle sizes were studied in transmission geometry using a high-resolution small-angle X-ray scattering setup at the P10 Coherence Beamline of the PETRA III synchrotron facility. The transformation of colloidal crystals to a melted state has been observed in a narrow temperature interval of less than 10 K.text/htmlIn situ X-ray crystallographic study of the structural evolution of colloidal crystals upon heatingtext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers903med@iucr.org9071600-5767X-ray characterization of Ge dots epitaxially grown on nanostructured Si islands on silicon-on-insulator substrateshttp://scripts.iucr.org/cgi-bin/paper?xz5001
On the way to integrate lattice mismatched semiconductors on Si(001), the Ge/Si heterosystem was used as a case study for the concept of compliant substrate effects that offer the vision to be able to integrate defect-free alternative semiconductor structures on Si. Ge nanoclusters were selectively grown by chemical vapour deposition on Si nano-islands on silicon-on-insulator (SOI) substrates. The strain states of Ge clusters and Si islands were measured by grazing-incidence diffraction using a laboratory-based X-ray diffraction technique. A tensile strain of up to 0.5% was detected in the Si islands after direct Ge deposition. Using a thin (∼10 nm) SiGe buffer layer between Si and Ge the tensile strain increases to 1.8%. Transmission electron microscopy studies confirm the absence of a regular grid of misfit dislocations in such structures. This clear experimental evidence for the compliance of Si nano-islands on SOI substrates opens a new integration concept that is not only limited to Ge but also extendable to semiconductors like III–V and II–VI materials.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Zaumseil, P.Kozlowski, G.Yamamoto, Y.Schubert, M.A.Schroeder, T.2013-08-01doi:10.1107/S0021889813003518International Union of CrystallographySelective epitaxial growth of Ge on nanostructured Si islands on silicon-on-insulator substrates is investigated by X-ray diffraction and transmission electron microscopy to prove the compliance effect between the materials and the structural perfection, especially under the use of a thin SiGe buffer layer.enNANOSTRUCTURED SI; GE HETEROEPITAXY; SILICON-ON-INSULATOR (SOI) SUBSTRATES; GRAZING-INCIDENCE X-RAY DIFFRACTION; TRANSMISSION ELECTRON MICROSCOPY (TEM)On the way to integrate lattice mismatched semiconductors on Si(001), the Ge/Si heterosystem was used as a case study for the concept of compliant substrate effects that offer the vision to be able to integrate defect-free alternative semiconductor structures on Si. Ge nanoclusters were selectively grown by chemical vapour deposition on Si nano-islands on silicon-on-insulator (SOI) substrates. The strain states of Ge clusters and Si islands were measured by grazing-incidence diffraction using a laboratory-based X-ray diffraction technique. A tensile strain of up to 0.5% was detected in the Si islands after direct Ge deposition. Using a thin (∼10 nm) SiGe buffer layer between Si and Ge the tensile strain increases to 1.8%. Transmission electron microscopy studies confirm the absence of a regular grid of misfit dislocations in such structures. This clear experimental evidence for the compliance of Si nano-islands on SOI substrates opens a new integration concept that is not only limited to Ge but also extendable to semiconductors like III–V and II–VI materials.text/htmlX-ray characterization of Ge dots epitaxially grown on nanostructured Si islands on silicon-on-insulator substratestext4462013-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers868med@iucr.org8731600-5767Improvements and considerations for size distribution retrieval from small-angle scattering data by Monte Carlo methodshttp://scripts.iucr.org/cgi-bin/paper?ce5145
Monte Carlo (MC) methods, based on random updates and the trial-and-error principle, are well suited to retrieve form-free particle size distributions from small-angle scattering patterns of non-interacting low-concentration scatterers such as particles in solution or precipitates in metals. Improvements are presented to existing MC methods, such as a non-ambiguous convergence criterion, nonlinear scaling of contributions to match their observability in a scattering measurement, and a method for estimating the minimum visibility threshold and uncertainties on the resulting size distributions.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Pauw, B.R.Pedersen, J.S.Tardif, S.Takata, M.Iversen, B.B.2013-04-01doi:10.1107/S0021889813001295International Union of CrystallographyImprovements are presented to existing Monte Carlo methods, allowing a particle size distribution to be retrieved from a scattering pattern, uncertainties to be estimated for the particle size distribution and the minimum number of particles required to make a measurable impact on the scattering pattern (the minimum visibility threshold) to be indicated for each feature in the distribution.enSTRUCTURE ANALYSIS; SMALL-ANGLE SCATTERING; MONTE CARLO METHODS; PARTICLE SIZE DISTRIBUTIONMonte Carlo (MC) methods, based on random updates and the trial-and-error principle, are well suited to retrieve form-free particle size distributions from small-angle scattering patterns of non-interacting low-concentration scatterers such as particles in solution or precipitates in metals. Improvements are presented to existing MC methods, such as a non-ambiguous convergence criterion, nonlinear scaling of contributions to match their observability in a scattering measurement, and a method for estimating the minimum visibility threshold and uncertainties on the resulting size distributions.text/htmlImprovements and considerations for size distribution retrieval from small-angle scattering data by Monte Carlo methodstext462http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-04-01research papers0021-8898med@iucr.org1600-5767Liesegang-like patterns of Toll crystals grown in gelhttp://scripts.iucr.org/cgi-bin/paper?he5568
Generating high-quality crystals remains a bottleneck in biological and materials sciences. Here a counter-diffusion method was used to improve the X-ray diffraction quality of the N-terminal domain of Drosophila melanogaster Toll receptor crystals. It was observed that crystallization occurred with a peculiar pattern along the capillary resembling Liesegang bands; this phenomenon is described at both macroscopic and atomic levels. It was found that bands appeared for native protein as well as for co-crystals of magic triangle (I3C)-bound protein even though they crystallize in different space groups. Crystallization occurred with a linear recurrence independent of the precipitant concentration and a protein-specific spacing coefficient. Bandwidth varied along the capillary, oscillating between large precipitation areas and single crystals. The reported data suggest that repetitive patterns can be generated with biological macromolecules in the presence of sodium malonate as a crystallization agent. A comparison with typical Liesegang patterns and the possible mechanism underlying this phenomenon are discussed.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Gangloff, M.Moreno, A.Gay, N.J.2013-04-01doi:10.1107/S0021889812051606International Union of CrystallographyThe observation of a repetitive pattern obtained for protein crystals formed by reaction–diffusion in capillary tubes is reported for the first time.enTOLL RECEPTOR; LIESEGANG RINGS; COUNTER-DIFFUSION CAPILLARY CRYSTALLIZATION; MALONATE; MAGIC TRIANGLE; I3C; OSTWALD RIPENING; REPETITIVE PATTERNSGenerating high-quality crystals remains a bottleneck in biological and materials sciences. Here a counter-diffusion method was used to improve the X-ray diffraction quality of the N-terminal domain of Drosophila melanogaster Toll receptor crystals. It was observed that crystallization occurred with a peculiar pattern along the capillary resembling Liesegang bands; this phenomenon is described at both macroscopic and atomic levels. It was found that bands appeared for native protein as well as for co-crystals of magic triangle (I3C)-bound protein even though they crystallize in different space groups. Crystallization occurred with a linear recurrence independent of the precipitant concentration and a protein-specific spacing coefficient. Bandwidth varied along the capillary, oscillating between large precipitation areas and single crystals. The reported data suggest that repetitive patterns can be generated with biological macromolecules in the presence of sodium malonate as a crystallization agent. A comparison with typical Liesegang patterns and the possible mechanism underlying this phenomenon are discussed.text/htmlLiesegang-like patterns of Toll crystals grown in geltext462http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-04-01research papers0021-8898med@iucr.org1600-5767Advanced Solid State Physics. By Philip Phillips. Pp. 402. 2nd ed. Cambridge University Press, 2012. Price (hardcover) GBP 45.00. ISBN 978-0-521-19490-7.http://scripts.iucr.org/cgi-bin/paper?pf0100
Copyright (c) 2013 International Union of Crystallographyurn:issn:0021-8898Eschrig, M.2013-02-01doi:10.1107/S0021889812050716International Union of CrystallographyenBOOK REVIEWtext/htmlAdvanced Solid State Physics. By Philip Phillips. Pp. 402. 2nd ed. Cambridge University Press, 2012. Price (hardcover) GBP 45.00. ISBN 978-0-521-19490-7.text461Copyright (c) 2013 International Union of CrystallographyJournal of Applied Crystallography2013-02-01287book reviews0021-8898med@iucr.org2881600-5767Directional pair distribution function for diffraction line profile analysis of atomistic modelshttp://scripts.iucr.org/cgi-bin/paper?ks5344
The concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren–Averbach method.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Leonardi, A.Leoni, M.Scardi, P.2013-02-01doi:10.1107/S0021889812050601International Union of CrystallographyThe concept of the directional pair distribution function is proposed for an atomistic level interpretation of the line profile broadening in powder diffraction patterns of nanocrystalline materials.enDIRECTIONAL PAIR DISTRIBUTION FUNCTION; LINE PROFILE ANALYSIS; WARREN-AVERBACH ANALYSIS; DISTORTION FIELDS; NANO-POLYCRYSTALLINE MICROSTRUCTURE; MOLECULAR DYNAMICSThe concept of the directional pair distribution function is proposed to describe line broadening effects in powder patterns calculated from atomistic models of nano-polycrystalline microstructures. The approach provides at the same time a description of the size effect for domains of any shape and a detailed explanation of the strain effect caused by the local atomic displacement. The latter is discussed in terms of different strain types, also accounting for strain field anisotropy and grain boundary effects. The results can in addition be directly read in terms of traditional line profile analysis, such as that based on the Warren–Averbach method.text/htmlDirectional pair distribution function for diffraction line profile analysis of atomistic modelstext461http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-02-0163research papers0021-8898med@iucr.org751600-5767Scherrer grain-size analysis adapted to grazing-incidence scattering with area detectors. Erratumhttp://scripts.iucr.org/cgi-bin/paper?ce5155
A poor divergence value in the paper by Smilgies [J. Appl. Cryst. (2009), 42, 1030–1034] is corrected.Copyright (c) 2013 International Union of Crystallographyurn:issn:0021-8898Smilgies, D.-M.2013-02-01doi:10.1107/S0021889812050054International Union of CrystallographyA poor divergence value in the paper by Smilgies [J. Appl. Cryst. (2009), 42, 1030–1034] is corrected.enSCHERRER FORMULA; GRAZING-INCIDENCE SMALL-ANGLE SCATTERING (GISAXS); GRAZING-INCIDENCE WIDE-ANGLE SCATTERING (GIWAXS); THIN FILMS; SOFT MATERIALSA poor divergence value in the paper by Smilgies [J. Appl. Cryst. (2009), 42, 1030–1034] is corrected.text/htmlScherrer grain-size analysis adapted to grazing-incidence scattering with area detectors. Erratumtext461Copyright (c) 2013 International Union of CrystallographyJournal of Applied Crystallography2013-02-01286addenda and errata0021-8898med@iucr.org2861600-5767The prolific polytypism of silicon carbidehttp://scripts.iucr.org/cgi-bin/paper?kk5117
A worked example of polytypism is presented, aimed at assisting undergraduates in the learning and instructors in the teaching of this topic. In particular, this crystallography concept, not necessarily obvious for beginners, is illustrated pedagogically using to that end the model case of the prolific polytypism of silicon carbide (SiC). On the basis of concepts that are easily assimilated by students (i.e. simple topological constraints) this article first presents a unified description of the polytypism phenomenon in SiC that allows one to understand without difficulty the existence of its numerous polytypic variants and how they develop. Then the various notations used to designate these different polytypes are described, and finally the crystal structures of the most common are discussed. This worked example is thus expected to contribute to motivating undergraduates in the study of a crystallography topic that often is not treated in sufficient depth in class.Copyright (c) 2013 International Union of Crystallographyurn:issn:0021-8898Ortiz, A.L.Sánchez-Bajo, F.Cumbrera, F.L.Guiberteau, F.2013-02-01doi:10.1107/S0021889812049151International Union of CrystallographyA worked example of polytypism is presented to motivate undergraduates in the study and instructors in the teaching of this crystallography topic.enSILICON CARBIDE; POLYTYPISM; POLYTYPESA worked example of polytypism is presented, aimed at assisting undergraduates in the learning and instructors in the teaching of this topic. In particular, this crystallography concept, not necessarily obvious for beginners, is illustrated pedagogically using to that end the model case of the prolific polytypism of silicon carbide (SiC). On the basis of concepts that are easily assimilated by students (i.e. simple topological constraints) this article first presents a unified description of the polytypism phenomenon in SiC that allows one to understand without difficulty the existence of its numerous polytypic variants and how they develop. Then the various notations used to designate these different polytypes are described, and finally the crystal structures of the most common are discussed. This worked example is thus expected to contribute to motivating undergraduates in the study of a crystallography topic that often is not treated in sufficient depth in class.text/htmlThe prolific polytypism of silicon carbidetext461Copyright (c) 2013 International Union of CrystallographyJournal of Applied Crystallography2013-02-01242teaching and education0021-8898med@iucr.org2471600-5767Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Sourcehttp://scripts.iucr.org/cgi-bin/paper?he5572
The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B4C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Classen, S.Hura, G.L.Holton, J.M.Rambo, R.P.Rodic, I.McGuire, P.J.Dyer, K.Hammel, M.Meigs, G.Frankel, K.A.Tainer, J.A.2013-02-01doi:10.1107/S0021889812048698International Union of CrystallographyThe SIBYLS beamline of the Advanced Light Source at Lawrence Berkeley National Laboratory is a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline. Key features and capabilities are described along with implementation and performance.enSMALL-ANGLE X-RAY SCATTERING (SAXS); MACROMOLECULAR CRYSTALLOGRAPHY (MX); SYNCHROTRON BEAMLINES; SIBYLSThe SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B4C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources.text/htmlImplementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Sourcetext461http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-02-011research papers0021-8898med@iucr.org131600-5767Experience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystalshttp://scripts.iucr.org/cgi-bin/paper?aj5204
The International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL. A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Tanley, S.W.M.Schreurs, A.M.M.Helliwell, J.R.Kroon-Batenburg, L.M.J.2013-02-01doi:10.1107/S0021889812044172International Union of CrystallographyA systematic analysis of diffraction data of 11 different lysozyme crystals (used for cisplatin and carboplatin binding studies), obtained with four diffraction data processing software packages and from two different diffractometers, serves as a pilot study for archiving raw diffraction data and associated metadata. The availability of the raw diffraction images allows for independent assessment of software packages.enDATA EXCHANGE; DATA ARCHIVING; METADATAThe International Union of Crystallography has for many years been advocating archiving of raw data to accompany structural papers. Recently, it initiated the formation of the Diffraction Data Deposition Working Group with the aim of developing standards for the representation of these data. A means of studying this issue is to submit exemplar publications with associated raw data and metadata. A recent study on the effects of dimethyl sulfoxide on the binding of cisplatin and carboplatin to histidine in 11 different lysozyme crystals from two diffractometers led to an investigation of the possible effects of the equipment and X-ray diffraction data processing software on the calculated occupancies and B factors of the bound Pt compounds. 35.3 Gb of data were transferred from Manchester to Utrecht to be processed with EVAL. A systematic comparison shows that the largest differences in the occupancies and B factors of the bound Pt compounds are due to the software, but the equipment also has a noticeable effect. A detailed description of and discussion on the availability of metadata is given. By making these raw diffraction data sets available via a local depository, it is possible for the diffraction community to make their own evaluation as they may wish.text/htmlExperience with exchange and archiving of raw data: comparison of data from two diffractometers and four software packages on a series of lysozyme crystalstext461http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2013-02-01108research papers0021-8898med@iucr.org1191600-5767A fast, simple and robust protocol for growing crystals in the lipidic cubic phasehttp://scripts.iucr.org/cgi-bin/paper?kk5118
A simple and inexpensive protocol for producing crystals in the sticky and viscous mesophase used for membrane protein crystallization by the in meso method is described. It provides crystals that appear within 15–30 min of setup at 293 K. The protocol gives the experimenter a convenient way of gaining familiarity and a level of comfort with the lipidic cubic mesophase, which can be daunting as a material when first encountered. Having used the protocol to produce crystals of the test protein, lysozyme, the experimenter can proceed with confidence to apply the method to more valuable membrane (and soluble) protein targets. The glass sandwich plates prepared using this robust protocol can further be used to practice harvesting and snap-cooling of in meso-grown crystals, to explore diffraction data collection with mesophase-embedded crystals, and for an assortment of quality control and calibration applications when used in combination with a crystallization robot.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Aherne, M.Lyons, J.A.Caffrey, M.2012-12-01doi:10.1107/S0021889812037880International Union of CrystallographyA simple robust manual protocol for producing crystals in the lipidic cubic phase in less than an hour is described. It is designed to provide newcomers to the in meso method for crystallizing membrane proteins with experience of preparing, handling and growing crystals in the sticky and viscous lipidic mesophase.enCRYSTALLIZATION; IN MESO CRYSTALLOGENESIS; LIPIDS; MEMBRANE PROTEINS; MESOPHASE; RECEPTORSA simple and inexpensive protocol for producing crystals in the sticky and viscous mesophase used for membrane protein crystallization by the in meso method is described. It provides crystals that appear within 15–30 min of setup at 293 K. The protocol gives the experimenter a convenient way of gaining familiarity and a level of comfort with the lipidic cubic mesophase, which can be daunting as a material when first encountered. Having used the protocol to produce crystals of the test protein, lysozyme, the experimenter can proceed with confidence to apply the method to more valuable membrane (and soluble) protein targets. The glass sandwich plates prepared using this robust protocol can further be used to practice harvesting and snap-cooling of in meso-grown crystals, to explore diffraction data collection with mesophase-embedded crystals, and for an assortment of quality control and calibration applications when used in combination with a crystallization robot.text/htmlA fast, simple and robust protocol for growing crystals in the lipidic cubic phasetext6452012-12-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898laboratory notesmed@iucr.org1600-5767Enhancing the volume and the optical quality of hen egg-white lysozyme crystals by coupling the salt concentration gradient crystallization method with a magnetic fieldhttp://scripts.iucr.org/cgi-bin/paper?he5553
The effect of coupling the salt concentration gradient crystallization method with the use of the paramagnetic salt MnCl2 and a magnetic field is reported. The use of a simple magnetic device is proposed to have a significant effect on hen egg-white lysozyme crystal growth. Large single crystals greater than 10 mm3 in volume with optical perfection were consistently obtained in this study.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Magay, E.Cho, S.J.Kim, S.A.2012-10-01doi:10.1107/S0021889812036060International Union of CrystallographyThe effect of coupling the salt concentration gradient crystallization method with the use of the paramagnetic salt MnCl2 and a magnetic field is reported. The use of a simple magnetic device is shown to have a significant effect on hen egg-white lysozyme crystal growth.enLYSOZYME; CRYSTALLIZATION; MAGNETIC FIELDS; OPTICAL PERFECTIONThe effect of coupling the salt concentration gradient crystallization method with the use of the paramagnetic salt MnCl2 and a magnetic field is reported. The use of a simple magnetic device is proposed to have a significant effect on hen egg-white lysozyme crystal growth. Large single crystals greater than 10 mm3 in volume with optical perfection were consistently obtained in this study.text/htmlEnhancing the volume and the optical quality of hen egg-white lysozyme crystals by coupling the salt concentration gradient crystallization method with a magnetic fieldtext5452012-10-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898laboratory notes1066med@iucr.org10681600-5767Nonlinear Mechanics of Crystals. By John D. Clayton. Pp. 700. Dordrecht, Heidelberg, London, New York: Springer, 2011. Price (hardcover) Euros 169.95. ISBN-978-94-007-0349-0.http://scripts.iucr.org/cgi-bin/paper?pf0098
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Paufler, P.2012-08-01doi:10.1107/S0021889812021139International Union of CrystallographyenBOOK RECEIVEDtext/htmlNonlinear Mechanics of Crystals. By John D. Clayton. Pp. 700. Dordrecht, Heidelberg, London, New York: Springer, 2011. Price (hardcover) Euros 169.95. ISBN-978-94-007-0349-0.text4452012-08-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898books receivedmed@iucr.org1600-5767From patterns to space groups and the eigensymmetry of crystallographic orbits: a reinterpretation of some symmetry diagrams in IUCr Teaching Pamphlet No. 14http://scripts.iucr.org/cgi-bin/paper?kk5107
The space group of a crystal pattern is the intersection group of the eigensymmetries of the crystallographic orbits corresponding to the occupied Wyckoff positions. Polar space groups without symmetry elements with glide or screw components smaller than 1/2 do not contain characteristic orbits and cannot be realized in patterns (structures) made by only one crystallographic type of object (atom). The space-group diagram of the general orbit for this type of group has an eigensymmetry that corresponds to a special orbit in a centrosymmetric supergroup of the generating group. This fact is often overlooked, as shown in the proposed solution for Plates (i)–(vi) of IUCr Teaching Pamphlet No. 14, and an alternative interpretation is given.Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Suescun, L.Nespolo, M.2012-08-01doi:10.1107/S002188981201998XInternational Union of CrystallographyThe common misinterpretation of a special orbit in centrosymmetric space groups as a general orbit in a polar subgroup is pointed out through some of the examples in IUCr Teaching Pamphlet No. 14, and an alternative interpretation is given.enSPACE GROUPS; EIGENSYMMETRIES; CRYSTALLOGRAPHIC ORBITS; IUCR TEACHING PAMPHLET NO. 14The space group of a crystal pattern is the intersection group of the eigensymmetries of the crystallographic orbits corresponding to the occupied Wyckoff positions. Polar space groups without symmetry elements with glide or screw components smaller than 1/2 do not contain characteristic orbits and cannot be realized in patterns (structures) made by only one crystallographic type of object (atom). The space-group diagram of the general orbit for this type of group has an eigensymmetry that corresponds to a special orbit in a centrosymmetric supergroup of the generating group. This fact is often overlooked, as shown in the proposed solution for Plates (i)–(vi) of IUCr Teaching Pamphlet No. 14, and an alternative interpretation is given.text/htmlFrom patterns to space groups and the eigensymmetry of crystallographic orbits: a reinterpretation of some symmetry diagrams in IUCr Teaching Pamphlet No. 14text4452012-08-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898teaching and educationmed@iucr.org1600-5767Three-dimensional Bragg coherent diffraction imaging of an extended ZnO crystalThis article also forms part of a special issue dedicated to advanced diffraction imaging methods of materials, which will be published as a virtual special issue of the journal in 2012/2013.http://scripts.iucr.org/cgi-bin/paper?nb5018
A complex three-dimensional quantitative image of an extended zinc oxide (ZnO) crystal has been obtained using Bragg coherent diffraction imaging integrated with ptychography. By scanning a 2.5 µm-long arm of a ZnO tetrapod across a 1.3 µm X-ray beam with fine step sizes while measuring a three-dimensional diffraction pattern at each scan spot, the three-dimensional electron density and projected displacement field of the entire crystal were recovered. The simultaneously reconstructed complex wavefront of the illumination combined with its coherence properties determined by a partial coherence analysis implemented in the reconstruction process provide a comprehensive characterization of the incident X-ray beam.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Huang, X.Harder, R.Leake, S.Clark, J.Robinson, I.2012-08-01doi:10.1107/S0021889812018900International Union of CrystallographyA complex three-dimensional quantitative image of an extended zinc oxide crystal has been obtained using Bragg coherent diffraction imaging integrated with ptychography.enTHREE-DIMENSIONAL QUANTITATIVE IMAGING; COHERENT DIFFRACTION IMAGING; PTYCHOGRAPHY; ZINC OXIDEA complex three-dimensional quantitative image of an extended zinc oxide (ZnO) crystal has been obtained using Bragg coherent diffraction imaging integrated with ptychography. By scanning a 2.5 µm-long arm of a ZnO tetrapod across a 1.3 µm X-ray beam with fine step sizes while measuring a three-dimensional diffraction pattern at each scan spot, the three-dimensional electron density and projected displacement field of the entire crystal were recovered. The simultaneously reconstructed complex wavefront of the illumination combined with its coherence properties determined by a partial coherence analysis implemented in the reconstruction process provide a comprehensive characterization of the incident X-ray beam.text/htmlThree-dimensional Bragg coherent diffraction imaging of an extended ZnO crystalThis article also forms part of a special issue dedicated to advanced diffraction imaging methods of materials, which will be published as a virtual special issue of the journal in 2012/2013.text4452012-08-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers778med@iucr.org7841600-5767PROSPERO: online prediction of crystallographic success from experimental results and sequencehttp://scripts.iucr.org/cgi-bin/paper?kk5105
The growth of diffracting crystals from purified proteins is often a major bottleneck in determining structures of biological and medical interest. The PROSPERO web server, http://skuld.bmsc.washington.edu/prospero, is intended both to provide a means of organizing the potentially large numbers of experimental characterizations measured from such proteins, and to provide useful guidance for structural biologists who have succeeded in purifying their target protein but have reached an impasse in the difficult and poorly understood process of turning purified protein into well diffracting crystals. These researchers need to decide which of many possible rescue options are worth pursuing, given finite resources. This choice is even more crucial when attempting to solve high-priority but relatively difficult structures of eukaryotic proteins. The site currently uses the HyGX1 predictor, which was trained and validated on protein samples from pathogenic protozoa (eukaryotes) using results from six types of experiment. PROSPERO allows users to store, analyze and display multiple results for each sample, to group samples into projects, and to share results and predictions with collaborators.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Zucker, F.H.Kim, H.Y.Merritt, E.A.2012-06-01doi:10.1107/S002188981201775XInternational Union of CrystallographyThe PROSPERO server analyzes sequence and experimental protein characterization results, then uses that analysis to predict crystallization outcome and suggest priorities for futher work on difficult targets. The server allows users to upload data from six types of experiment, to organize those data by sample and project, and to share those data with collaborators.enPROTEIN CRYSTALLOGRAPHY; PROTEIN CHARACTERIZATION; PROSPERO; COMPUTER PROGRAMSThe growth of diffracting crystals from purified proteins is often a major bottleneck in determining structures of biological and medical interest. The PROSPERO web server, http://skuld.bmsc.washington.edu/prospero, is intended both to provide a means of organizing the potentially large numbers of experimental characterizations measured from such proteins, and to provide useful guidance for structural biologists who have succeeded in purifying their target protein but have reached an impasse in the difficult and poorly understood process of turning purified protein into well diffracting crystals. These researchers need to decide which of many possible rescue options are worth pursuing, given finite resources. This choice is even more crucial when attempting to solve high-priority but relatively difficult structures of eukaryotic proteins. The site currently uses the HyGX1 predictor, which was trained and validated on protein samples from pathogenic protozoa (eukaryotes) using results from six types of experiment. PROSPERO allows users to store, analyze and display multiple results for each sample, to group samples into projects, and to share results and predictions with collaborators.text/htmlPROSPERO: online prediction of crystallographic success from experimental results and sequencetext3452012-06-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898computer programs598med@iucr.org6021600-5767Graphical tools for macromolecular crystallography in PHENIXhttp://scripts.iucr.org/cgi-bin/paper?kk5108
A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Echols, N.Grosse-Kunstleve, R.W.Afonine, P.V.Bunkoczi, G.Chen, V.B.Headd, J.J.McCoy, A.J.Moriarty, N.W.Read, R.J.Richardson, D.C.Richardson, J.S.Terwilliger, T.C.Adams, P.D.2012-06-01doi:10.1107/S0021889812017293International Union of CrystallographyThe foundations and current features of a widely used graphical user interface for macromolecular crystallography are described.enMACROMOLECULAR CRYSTALLOGRAPHY; GRAPHICAL USER INTERFACES; PHENIXA new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified.text/htmlGraphical tools for macromolecular crystallography in PHENIXtext3452012-06-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898computer programs581med@iucr.org5861600-5767Valentin Ivanovich Simonov (1930–2012)http://scripts.iucr.org/cgi-bin/paper?es0395
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Group of colleagues2012-06-01doi:10.1107/S0021889812015725International Union of CrystallographyenOBITUARYtext/htmlValentin Ivanovich Simonov (1930–2012)text3452012-06-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898crystallographers611med@iucr.org6111600-5767Materials Science of DNA. Edited by J.-I. Jin and J. Grote. Pp. 326. Boca Raton: CRC Press, Taylor & Francis Group, 2012. Price (hardcover) GBP 76.99. ISBN 978-1-398-2741-3.http://scripts.iucr.org/cgi-bin/paper?pf0095
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Pompe, W.2012-06-01doi:10.1107/S0021889812014434International Union of CrystallographyenBOOK REVIEWtext/htmlMaterials Science of DNA. Edited by J.-I. Jin and J. Grote. Pp. 326. Boca Raton: CRC Press, Taylor & Francis Group, 2012. Price (hardcover) GBP 76.99. ISBN 978-1-398-2741-3.text3452012-06-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898book reviews612med@iucr.org6121600-5767New developments in the ATSAS program package for small-angle scattering data analysishttp://scripts.iucr.org/cgi-bin/paper?fs5015
New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Petoukhov, M.V.Franke, D.Shkumatov, A.V.Tria, G.Kikhney, A.G.Gajda, M.Gorba, C.Mertens, H.D.T.Konarev, P.V.Svergun, D.I.2012-03-15doi:10.1107/S0021889812007662International Union of CrystallographyThe paper presents new developments and amendments to the ATSAS package (version 2.4) for processing and analysis of isotropic small-angle scattering data.enISOTROPIC SCATTERING; SMALL-ANGLE SCATTERING; DATA ANALYSIS; BIOLOGICAL MACROMOLECULES; STRUCTURAL MODELLING; ATSAS; COMPUTER PROGRAMSNew developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small-angle X-ray and neutron scattering data are described. They include (i) multiplatform data manipulation and display tools, (ii) programs for automated data processing and calculation of overall parameters, (iii) improved usage of high- and low-resolution models from other structural methods, (iv) new algorithms to build three-dimensional models from weakly interacting oligomeric systems and complexes, and (v) enhanced tools to analyse data from mixtures and flexible systems. The new ATSAS release includes installers for current major platforms (Windows, Linux and Mac OSX) and provides improved indexed user documentation. The web-related developments, including a user discussion forum and a widened online access to run ATSAS programs, are also presented.text/htmlNew developments in the ATSAS program package for small-angle scattering data analysistext2452012-03-15Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898computer programs342med@iucr.org3501600-5767Introduction to Nonlinear Optics. By Geoffrey New. Pp. xv+257. Cambridge: University Press, 2011. Price (hardcover) GBP 45.00, USD 75.00. ISBN-9780521877015.http://scripts.iucr.org/cgi-bin/paper?pf0096
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Paufler, P.2012-06-01doi:10.1107/S0021889812006607International Union of CrystallographyenBOOK RECEIVEDtext/htmlIntroduction to Nonlinear Optics. By Geoffrey New. Pp. xv+257. Cambridge: University Press, 2011. Price (hardcover) GBP 45.00, USD 75.00. ISBN-9780521877015.text453Copyright (c) 2012 International Union of CrystallographyJournal of Applied Crystallography2012-06-01books received0021-8898med@iucr.org1600-5767Hans Dachs (1927–2011)http://scripts.iucr.org/cgi-bin/paper?es0394
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Steiner, M.2012-04-01doi:10.1107/S0021889812006668International Union of CrystallographyenOBITUARYtext/htmlHans Dachs (1927–2011)text2452012-04-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898crystallographers373med@iucr.org3731600-5767CrystalEye: automated aggregation, semantification and dissemination of the world's open crystallographic datahttp://scripts.iucr.org/cgi-bin/paper?he5533
CrystalEye automatically aggregates crystallographic data from web resources (the supplementary data to articles on publishers' web sites) into a structured XML-based repository, and then adds value to that open data by providing methods to easily browse, search and to keep up-to-date with the latest published information.Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Day, N.Downing, J.Adams, S.England, N.W.Murray-Rust, P.2012-04-01doi:10.1107/S0021889812006462International Union of CrystallographyAn automatic system for the aggregation, semantification and presentation of open crystallographic data is presented.enCIF; XML; CML; CRYSTALEYE; COMPUTER PROGRAMSCrystalEye automatically aggregates crystallographic data from web resources (the supplementary data to articles on publishers' web sites) into a structured XML-based repository, and then adds value to that open data by providing methods to easily browse, search and to keep up-to-date with the latest published information.text/htmlCrystalEye: automated aggregation, semantification and dissemination of the world's open crystallographic datatext2452012-04-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898CIF applications316med@iucr.org3231600-5767Alexander McLeod Mathieson (1920–2011)http://scripts.iucr.org/cgi-bin/paper?es0393
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Wilkins, S.Stevenson, A.Gulbis, J.2012-04-01doi:10.1107/S0021889812005213International Union of CrystallographyenOBITUARYtext/htmlAlexander McLeod Mathieson (1920–2011)text2452012-04-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898crystallographers371med@iucr.org3721600-5767Crystal Engineering. A Textbook. By Gautam R. Desiraju, Jagadese J. Vittal and Arunachalam Ramanan. Pp. xiv+216. Singapore: World Scientific, 2011. Price (paperback) USD 49. ISBN-978 981 4366 86 1.http://scripts.iucr.org/cgi-bin/paper?pf0094
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Paufler, P.2012-04-01doi:10.1107/S0021889812001938International Union of CrystallographyenBOOK RECEIVEDtext/htmlCrystal Engineering. A Textbook. By Gautam R. Desiraju, Jagadese J. Vittal and Arunachalam Ramanan. Pp. xiv+216. Singapore: World Scientific, 2011. Price (paperback) USD 49. ISBN-978 981 4366 86 1.text2452012-04-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898books receivedmed@iucr.org1600-5767A simplified invariant line analysis for face-centred cubic/body-centred cubic precipitation systems. Erratumhttp://scripts.iucr.org/cgi-bin/paper?ks5310
Errors in the paper by Liu, Waclawik & Luo [J. Appl. Cryst. (2010), 43, 448–454] are corrected.Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Liu, H.Waclawik, E.R.Luo, C.2012-02-01doi:10.1107/S0021889811055087International Union of CrystallographyErrors in the paper by Liu, Waclawik & Luo [J. Appl. Cryst. (2010), 43, 448–454] are corrected.enTRANSFORMATIONS; INVARIANT LINE ANALYSIS; PRECIPITATION; HABIT PLANES; ORIENTATION RELATIONSHIPSErrors in the paper by Liu, Waclawik & Luo [J. Appl. Cryst. (2010), 43, 448–454] are corrected.text/htmlA simplified invariant line analysis for face-centred cubic/body-centred cubic precipitation systems. Erratumtext1452012-02-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898addenda and errata141med@iucr.org1411600-5767A manual low-cost protein-crystallization plate jig for in situ diffraction in the home laboratoryhttp://scripts.iucr.org/cgi-bin/paper?fs5009
A prototype jig to attach a protein crystallization plate to a standard X-ray goniometer has been designed and constructed in partnership with an engineering firm. This allows a low-cost implementation of in situ diffraction using the available home-laboratory X-ray source.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Hargreaves, D.2012-02-01doi:10.1107/S0021889811052654International Union of CrystallographyA prototype jig to attach a protein crystallization plate to a standard X-ray goniometer has been designed and constructed. This allows a low-cost implementation of in situ diffraction using the available home-laboratory X-ray source.enIN SITU DIFFRACTION SCREENING; CRYSTALLIZATION PLATES; CRYSTAL QUALITY; ROOM-TEMPERATURE DIFFRACTIONA prototype jig to attach a protein crystallization plate to a standard X-ray goniometer has been designed and constructed in partnership with an engineering firm. This allows a low-cost implementation of in situ diffraction using the available home-laboratory X-ray source.text/htmlA manual low-cost protein-crystallization plate jig for in situ diffraction in the home laboratorytext1452012-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898laboratory notes138med@iucr.org1401600-5767Concepts and Methods of 2D Infrared Spectroscopy. By Peter Hamm and Martin Zanni. Pp. 296, 124 illustrations, 71 exercises. Cambridge University Press, 2011. Price (hardcover) 99.00 USD. ISBN 978-1-107-00005-6.http://scripts.iucr.org/cgi-bin/paper?pf0090
Copyright (c) 2012 International Union of Crystallographyurn:issn:0021-8898Vtyurin, A.2012-02-01doi:10.1107/S0021889811051429International Union of Crystallographyentext/htmlConcepts and Methods of 2D Infrared Spectroscopy. By Peter Hamm and Martin Zanni. Pp. 296, 124 illustrations, 71 exercises. Cambridge University Press, 2011. Price (hardcover) 99.00 USD. ISBN 978-1-107-00005-6.text1452012-02-01Journal of Applied CrystallographyCopyright (c) 2012 International Union of Crystallography0021-8898book reviews148med@iucr.org1491600-5767ShelXle: a Qt graphical user interface for SHELXLhttp://scripts.iucr.org/cgi-bin/paper?kk5092
ShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Hübschle, C.B.Sheldrick, G.M.Dittrich, B.2011-12-01doi:10.1107/S0021889811043202International Union of CrystallographyShelXle is a user-friendly graphical user interface for SHELXL.enMOLECULE VIEWERS; ELECTRON DENSITY MAPS; SYNTAX HIGHLIGHTING; ISOSURFACES; SHELX; SHELXL; GRAPHICAL USER INTERFACESShelXle is a graphical user interface for SHELXL [Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features of ShelXle include intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions. ShelXle is completely compatible with all features of SHELXL and is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.text/htmlShelXle: a Qt graphical user interface for SHELXLtext6442011-12-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898computer programs1281med@iucr.org12841600-5767ANODE: anomalous and heavy-atom density calculationhttp://scripts.iucr.org/cgi-bin/paper?fs5005
The new program ANODE estimates anomalous or heavy-atom density by reversing the usual procedure for experimental phase determination by methods such as single- and multiple-wavelength anomalous diffraction and single isomorphous replacement anomalous scattering. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase. The required native phase is calculated from the information in a Protein Data Bank file of the structure. The resulting density enables even very weak anomalous scatterers such as sulfur to be located. Potential applications include the identification of unknown atoms and the validation of molecular replacement solutions.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Thorn, A.Sheldrick, G.M.2011-12-01doi:10.1107/S0021889811041768International Union of CrystallographyThe program ANODE determines anomalous (or heavy-atom) densities.enANOMALOUS DENSITY; HEAVY-ATOM DENSITY; EXPERIMENTAL PHASING; COMPUTER PROGRAMSThe new program ANODE estimates anomalous or heavy-atom density by reversing the usual procedure for experimental phase determination by methods such as single- and multiple-wavelength anomalous diffraction and single isomorphous replacement anomalous scattering. Instead of adding a phase shift to the heavy-atom phases to obtain a starting value for the native protein phase, this phase shift is subtracted from the native phase to obtain the heavy-atom substructure phase. The required native phase is calculated from the information in a Protein Data Bank file of the structure. The resulting density enables even very weak anomalous scatterers such as sulfur to be located. Potential applications include the identification of unknown atoms and the validation of molecular replacement solutions.text/htmlANODE: anomalous and heavy-atom density calculationtext6442011-12-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898computer programs1285med@iucr.org12871600-5767iotbx.cif: a comprehensive CIF toolboxhttp://scripts.iucr.org/cgi-bin/paper?hx5135
iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Gildea, R.J.Bourhis, L.J.Dolomanov, O.V.Grosse-Kunstleve, R.W.Puschmann, H.Adams, P.D.Howard, J.A.K.2011-12-01doi:10.1107/S0021889811041161International Union of Crystallographyiotbx.cif is a comprehensive toolbox for the development of applications that make use of the CIF format.enIOTBX.CIF; CCTBX; CIF; COMPUTER PROGRAMSiotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.text/htmliotbx.cif: a comprehensive CIF toolboxtext6442011-12-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898CIF applications1259med@iucr.org12631600-5767Le cristal et ses doubles. By Jean-Claude Boulliard. Pp. 347. Paris: CNRS Éditions, 2010. In French. Price (hardcover) EUR 59. ISBN 978-2-271-07049-4.http://scripts.iucr.org/cgi-bin/paper?pf0084
Copyright (c) 2011 International Union of Crystallographyurn:issn:0021-8898Klapper, H.Hahn, Th.2011-12-01doi:10.1107/S0021889811039902International Union of Crystallographyentext/htmlLe cristal et ses doubles. By Jean-Claude Boulliard. Pp. 347. Paris: CNRS Éditions, 2010. In French. Price (hardcover) EUR 59. ISBN 978-2-271-07049-4.text6442011-12-01Journal of Applied CrystallographyCopyright (c) 2011 International Union of Crystallography0021-8898book reviews1300med@iucr.org13001600-5767Supercritical carbon dioxide behaviour in porous silica aerogel. Erratumhttp://scripts.iucr.org/cgi-bin/paper?ko9123
Errors in the paper by Ciccariello, Melnichenko & He [J. Appl. Cryst. (2011), 44, 43–51] are corrected.Copyright (c) 2011 International Union of Crystallographyurn:issn:0021-8898Ciccariello, S.Melnichenko, Y.B.He, L.2011-10-01doi:10.1107/S0021889811035631International Union of CrystallographyErrors in the paper by Ciccariello, Melnichenko & He [J. Appl. Cryst. (2011), 44, 43–51] are corrected.enSUPERCRITICAL CARBON DIOXIDE; POROUS SILICA AEROGELS; SMALL-ANGLE NEUTRON SCATTERINGErrors in the paper by Ciccariello, Melnichenko & He [J. Appl. Cryst. (2011), 44, 43–51] are corrected.text/htmlSupercritical carbon dioxide behaviour in porous silica aerogel. Erratumtext445Copyright (c) 2011 International Union of CrystallographyJournal of Applied Crystallography2011-10-011137addenda and errata0021-8898med@iucr.org11371600-5767Simon Charles Moss (1934–2011)http://scripts.iucr.org/cgi-bin/paper?es0387
Copyright (c) 2011 International Union of Crystallographyurn:issn:0021-8898Schönfeld, B.Wochner, P.2011-08-01doi:10.1107/S0021889811019091International Union of CrystallographyenOBITUARYtext/htmlSimon Charles Moss (1934–2011)text444Copyright (c) 2011 International Union of CrystallographyJournal of Applied Crystallography2011-08-011crystallographers0021-8898med@iucr.org1600-5767Combined Analysis. By D. Chateigner. Pp. xviii + 497, 188 figures + 46 tables. London, Hoboken: ISTE Ltd, Wiley, 2010. Price (hardcover) EUR 132. ISBN 978-1-84821-198-8.http://scripts.iucr.org/cgi-bin/paper?pf0081
Copyright (c) 2011 International Union of Crystallographyurn:issn:0021-8898Esling, C.2011-08-01doi:10.1107/S0021889811017985International Union of CrystallographyenBOOK REVIEWStext/htmlCombined Analysis. By D. Chateigner. Pp. xviii + 497, 188 figures + 46 tables. London, Hoboken: ISTE Ltd, Wiley, 2010. Price (hardcover) EUR 132. ISBN 978-1-84821-198-8.text444Copyright (c) 2011 International Union of CrystallographyJournal of Applied Crystallography2011-08-011book reviews0021-8898med@iucr.org11600-5767New software for statistical analysis of Cambridge Structural Database datahttp://scripts.iucr.org/cgi-bin/paper?he5529
A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Sykes, R.A.McCabe, P.Allen, F.H.Battle, G.M.Bruno, I.J.Wood, P.A.2011-08-01doi:10.1107/S0021889811014622International Union of CrystallographyA new piece of software for statistical analysis of geometrical, chemical and crystallographic data within the Cambridge Structural Database System is described. This software has been written specifically to deal with chemical structure data and crucially provides simultaneous visualization of the three-dimensional structural information.enDATA ANALYSIS; COMPUTER PROGRAMS; CAMBRIDGE STRUCTURAL DATABASE; SUBSTRUCTURE; VISTAA collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments.text/htmlNew software for statistical analysis of Cambridge Structural Database datatext444http://creativecommons.org/licenses/by/2.0/ukJournal of Applied Crystallography2011-08-01882computer programs0021-8898med@iucr.org8861600-5767CIFXML: a schema and toolkit for managing CIFs in XMLhttp://scripts.iucr.org/cgi-bin/paper?he5526
CIFXML applies the XML strategies and technologies to create a general interface for processing CIF documents that conform to the CIF syntax and DDL1. Both a DTD and an XML schema for CIFs are presented. CIFs can be read, edited, validated syntactically, sorted, normalized, filtered, stored as an XML document object model, transformed and output. CIFXOM provides an easy way of converting CIFs to XML and vice versa using Java.Copyright (c) 2011 International Union of Crystallographyurn:issn:0021-8898Day, N.E.Murray-Rust, P.Tyrrell, S.M.2011-06-01doi:10.1107/S0021889811011058International Union of CrystallographyA toolkit for conversion of CIF documents into complete semantic XML documents is presented.enCIF; XML; CIFXML; CML; SAX; DOM; XOM; JAVA; DTD; SCHEMA; COMPUTER PROGRAMS; CIFXOMCIFXML applies the XML strategies and technologies to create a general interface for processing CIF documents that conform to the CIF syntax and DDL1. Both a DTD and an XML schema for CIFs are presented. CIFs can be read, edited, validated syntactically, sorted, normalized, filtered, stored as an XML document object model, transformed and output. CIFXOM provides an easy way of converting CIFs to XML and vice versa using Java.text/htmlCIFXML: a schema and toolkit for managing CIFs in XMLtext3442011-06-01Journal of Applied CrystallographyCopyright (c) 2011 International Union of Crystallography0021-8898CIF applications628med@iucr.org6341600-5767Incoherent neutron scattering from multi-element materialshttp://scripts.iucr.org/cgi-bin/paper?kk5083
In a neutron diffraction measurement, including small-angle scattering, there is generally a featureless (i.e. Q-independent) component due to incoherent scattering. This scattering contains no information about the atomic structure or structure on any scale. There may also be featureless scattering that arises from atomic disorder in multi-element materials. This scattering is sometimes referred to as compositional or mixture incoherent scattering. However, this designation is misleading. A much better designation is diffuse coherent scattering. Here the differences and distinguishing characteristics of incoherent scattering vis-à-vis diffuse coherent scattering due to atomic disorder are delineated and demonstrated experimentally.Copyright (c) 2011 International Union of Crystallographyurn:issn:0021-8898Glinka, C.J.2011-06-01doi:10.1107/S0021889811008223International Union of CrystallographyThe differences and distinguishing characteristics of incoherent scattering vis-à-vis diffuse coherent scattering due to atomic disorder are delineated and demonstrated experimentally.enNEUTRON SCATTERING; DIFFUSE SCATTERING; INCOHERENT SCATTERING; ATOMIC DISORDER; ISOTOPES; NUCLEAR SPIN; LAUE MONOTONIC SCATTERING; ISOTOPE EXCHANGE; DEUTERATED SOLVENTSIn a neutron diffraction measurement, including small-angle scattering, there is generally a featureless (i.e. Q-independent) component due to incoherent scattering. This scattering contains no information about the atomic structure or structure on any scale. There may also be featureless scattering that arises from atomic disorder in multi-element materials. This scattering is sometimes referred to as compositional or mixture incoherent scattering. However, this designation is misleading. A much better designation is diffuse coherent scattering. Here the differences and distinguishing characteristics of incoherent scattering vis-à-vis diffuse coherent scattering due to atomic disorder are delineated and demonstrated experimentally.text/htmlIncoherent neutron scattering from multi-element materialstext3442011-06-01Journal of Applied CrystallographyCopyright (c) 2011 International Union of Crystallography0021-8898teaching and education618med@iucr.org6241600-5767Evaluation of the Bruker SMART X2S: crystallography for the nonspecialist?http://scripts.iucr.org/cgi-bin/paper?kk5074
An evaluation of the Bruker SMART X2S for the collection of crystallographic diffraction data, structure solution and refinement is carried out with a variety of materials with different electron densities, presenting some of the successes and challenges of automation in chemical crystallography.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Eccles, K.S.Stokes, S.P.Daly, C.A.Barry, N.M.McSweeney, S.P.O'Neill, D.J.Kelly, D.M.Jennings, W.B.Ní Dhubhghaill, O.M.Moynihan, H.A.Maguire, A.R.Lawrence, S.E.2011-02-01doi:10.1107/S0021889810042561International Union of CrystallographyAn evaluation of the Bruker SMART X2S for the collection of crystallographic diffraction data, structure solution and refinement is carried out with a variety of materials with different electron densities, presenting some of the successes and challenges of automation in chemical crystallography.enBRUKER SMART X2S; INSTRUMENTATION; AUTOMATIONAn evaluation of the Bruker SMART X2S for the collection of crystallographic diffraction data, structure solution and refinement is carried out with a variety of materials with different electron densities, presenting some of the successes and challenges of automation in chemical crystallography.text/htmlEvaluation of the Bruker SMART X2S: crystallography for the nonspecialist?text1442011-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898short communications213med@iucr.org2151600-5767MoleCoolQt – a molecule viewer for charge-density researchhttp://scripts.iucr.org/cgi-bin/paper?he5499
MoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Hübschle, C.B.Dittrich, B.2011-02-01doi:10.1107/S0021889810042482International Union of CrystallographyMoleCoolQt is a molecule viewer designed for experimental charge density studies with a user-friendly graphical user interface.enMOLECOOLQT; CHARGE DENSITY; VISUALIZATION SOFTWAREMoleCoolQt is a molecule viewer for charge-density research. Features include the visualization of local atomic coordinate systems in multipole refinements based on the Hansen and Coppens formalism as implemented, for example, in the XD suite. Residual peaks and holes from XDfft are translated so that they appear close to the nearest atom of the asymmetric unit. Critical points from a topological analysis of the charge density can also be visualized. As in the program MolIso, color-mapped isosurfaces can be generated with a simple interface. Apart from its visualization features the program interactively helps in assigning local atomic coordinate systems and local symmetry, which can be automatically detected and altered. Dummy atoms – as sometimes required for local atomic coordinate systems – are calculated on demand; XD system files are updated after changes. When using the invariom database, potential scattering factor assignment problems can be resolved by the use of an interactive dialog. The following file formats are supported: XD, MoPro, SHELX, GAUSSIAN (com, FChk, cube), CIF and PDB. MoleCoolQt is written in C++ using the Qt4 library, has a user-friendly graphical user interface, and is available for several flavors of Linux, Windows and MacOS.text/htmlMoleCoolQt – a molecule viewer for charge-density researchtext1442011-02-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898computer programs238med@iucr.org2401600-5767Citations in supplementary materialhttp://scripts.iucr.org/cgi-bin/paper?me0428
Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Weiss, M.S.Einspahr, H.Baker, E.N.Dauter, Z.Kaysser-Pyzalla Kaysser-Pyzalla, A. R.Kostorz, G.Larsen, S.2010-11-16doi:10.1107/S0021889810041804International Union of CrystallographyThe problem of undercounting of citations that are published only in supplementary material is studied for the journals Nature, Science, Cell and the Proceedings of the National Academy of Sciences (USA).enCITATIONS; SUPPLEMENTARY MATERIAL; EDITORIALtext/htmlCitations in supplementary materialtext6432010-11-16Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898editorial1285med@iucr.org12861600-5767Versatile in situ powder X-ray diffraction cells for solid–gas investigationshttp://scripts.iucr.org/cgi-bin/paper?db5089
This paper describes new sample cells and techniques for in situ powder X-ray diffraction specifically designed for gas absorption studies up to ca 300 bar (1 bar = 100 000 Pa) gas pressure. The cells are for multipurpose use, in particular the study of solid–gas reactions in dosing or flow mode, but can also handle samples involved in solid–liquid–gas studies. The sample can be loaded into a single-crystal sapphire (Al2O3) capillary, or a quartz (SiO2) capillary closed at one end. The advantages of a sapphire single-crystal cell with regard to rapid pressure cycling are discussed, and burst pressures are calculated and measured to be ∼300 bar. An alternative and simpler cell based on a thin-walled silicate or quartz glass capillary, connected to a gas source via a VCR fitting, enables studies up to ∼100 bar. Advantages of the two cell types are compared and their applications are illustrated by case studies.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Jensen, T.R.Nielsen, T.K.Filinchuk, Y.Jørgensen, J.-E.Cerenius, Y.Gray, E.M.Webb, C.J.2010-12-01doi:10.1107/S0021889810038148International Union of CrystallographyTwo multipurpose sample cells of quartz (SiO2) or sapphire (Al2O3) capillaries, developed for the study of solid–gas reactions in dosing or flow mode, are presented. They allow fast change of pressure up to 100 or 300 bar (1 bar = 100 000 Pa) and can also handle solid–liquid–gas studies.enPOWDER X-RAY DIFFRACTION; X-RAY DIFFRACTION CELLS; SOLID-GAS REACTIONS; HYDROGEN ABSORPTIONThis paper describes new sample cells and techniques for in situ powder X-ray diffraction specifically designed for gas absorption studies up to ca 300 bar (1 bar = 100 000 Pa) gas pressure. The cells are for multipurpose use, in particular the study of solid–gas reactions in dosing or flow mode, but can also handle samples involved in solid–liquid–gas studies. The sample can be loaded into a single-crystal sapphire (Al2O3) capillary, or a quartz (SiO2) capillary closed at one end. The advantages of a sapphire single-crystal cell with regard to rapid pressure cycling are discussed, and burst pressures are calculated and measured to be ∼300 bar. An alternative and simpler cell based on a thin-walled silicate or quartz glass capillary, connected to a gas source via a VCR fitting, enables studies up to ∼100 bar. Advantages of the two cell types are compared and their applications are illustrated by case studies.text/htmlVersatile in situ powder X-ray diffraction cells for solid–gas investigationstext6432010-12-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1456med@iucr.org14631600-5767A general method to determine twinning elementshttp://scripts.iucr.org/cgi-bin/paper?cg5155
The fundamental theory of crystal twinning has been long established, leading to a significant advance in understanding the nature of this physical phenomenon. However, there remains a substantial gap between the elaborate theory and the practical determination of twinning elements. This paper proposes a direct and simple method – valid for any crystal structure and based on the minimum shear criterion – to calculate various twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. Without additional efforts, it is generally applicable to identify and predict possible twinning modes occurring in a variety of crystalline solids. Therefore, the present method is a promising tool to characterize twinning elements, especially for those materials with complex crystal structure.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Zhang, Y.Li, Z.Esling, C.Muller, J.Zhao, X.Zuo, L.2010-12-01doi:10.1107/S0021889810037180International Union of CrystallographyBased on the minimum shear criterion, a direct and simple method is proposed to calculate twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. It is generic and applicable to any crystal structure.enTWINNING; MINIMUM SHEAR; INTERFACE STRUCTURE; TRANSMISSION ELECTRON MICROSCOPY; SCANNING ELECTRON MICROSCOPY/ELECTRON BACKSCATTER DIFFRACTIONThe fundamental theory of crystal twinning has been long established, leading to a significant advance in understanding the nature of this physical phenomenon. However, there remains a substantial gap between the elaborate theory and the practical determination of twinning elements. This paper proposes a direct and simple method – valid for any crystal structure and based on the minimum shear criterion – to calculate various twinning elements from the experimentally determined twinning plane for Type I twins or the twinning direction for Type II twins. Without additional efforts, it is generally applicable to identify and predict possible twinning modes occurring in a variety of crystalline solids. Therefore, the present method is a promising tool to characterize twinning elements, especially for those materials with complex crystal structure.text/htmlA general method to determine twinning elementstext6432010-12-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1426med@iucr.org14301600-5767Lachlan M. D. Cranswick (1968–2010)http://scripts.iucr.org/cgi-bin/paper?es0383
Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Scarlett, N.Cockcroft, J.Swainson, I.2010-10-01doi:10.1107/S0021889810035971International Union of Crystallographyentext/htmlLachlan M. D. Cranswick (1968–2010)text51432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898crystallographers1134med@iucr.org11341600-5767RapiData: a practical course in macromolecular X-ray diffraction data measurement and structure solving at the NSLShttp://scripts.iucr.org/cgi-bin/paper?kk5071
RapiData provides two days of high-level lectures, then two more of experimental work on several beamlines of the National Synchrotron Light Source, for about 50 students. Students are invited to bring their own research projects for measurement, and about half of them do. The students frequently solve half a dozen structures during the course. Tutorials by the lecturers run throughout the data-collection period. The crystal-preparation laboratory is popular for tutorials and practice, and often there is a beamline available for practice. This article provides details about the organization of the course and tells some of the reasons for its success.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Sweet, R.M.Soares, A.2010-10-01doi:10.1107/S0021889810034527International Union of CrystallographyRapiData provides two days of high-level lectures, then two more of experimental work on several beamlines of the National Synchrotron Light Source, for about 50 students. This article provides details about the organization of the course and tells some of the reasons for its success.enCRYSTALLOGRAPHIC EDUCATION; RAPIDATA; MACROMOLECULAR CRYSTALLOGRAPHY; NSLSRapiData provides two days of high-level lectures, then two more of experimental work on several beamlines of the National Synchrotron Light Source, for about 50 students. Students are invited to bring their own research projects for measurement, and about half of them do. The students frequently solve half a dozen structures during the course. Tutorials by the lecturers run throughout the data-collection period. The crystal-preparation laboratory is popular for tutorials and practice, and often there is a beamline available for practice. This article provides details about the organization of the course and tells some of the reasons for its success.text/htmlRapiData: a practical course in macromolecular X-ray diffraction data measurement and structure solving at the NSLStext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1238med@iucr.org1241Observations on online educational materials for powder diffraction crystallography softwarehttp://scripts.iucr.org/cgi-bin/paper?kk5072
This article presents a series of approaches used to educate potential users of crystallographic software for powder diffraction. The approach that has been most successful in the author's opinion is the web lecture, where an audio presentation is coupled to a video-like record of the contents of the presenter's computer screen.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Toby, B.H.2010-10-01doi:10.1107/S0021889810034382International Union of CrystallographyThis article provides a commentary on the successes and shortcomings of the author's educational outreach approaches for powder diffraction crystallographic software and techniques.enCRYSTALLOGRAPHIC EDUCATION; ONLINE EDUCATIONAL MATERIALS; COMPUTER PROGRAMS; POWDER DIFFRACTIONThis article presents a series of approaches used to educate potential users of crystallographic software for powder diffraction. The approach that has been most successful in the author's opinion is the web lecture, where an audio presentation is coupled to a video-like record of the contents of the presenter's computer screen.text/htmlObservations on online educational materials for powder diffraction crystallography softwaretext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1271med@iucr.org1275Crystallography education and training for the 21st centuryhttp://scripts.iucr.org/cgi-bin/paper?me0424
Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Kantardjieff, K.A.Kaysser-Pyzalla, A.R.Spadon, P.2010-10-01doi:10.1107/S0021889810034357International Union of CrystallographyenEDITORIAL; CRYSTALLOGRAPHIC EDUCATIONtext/htmlCrystallography education and training for the 21st centurytext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898editorial1137med@iucr.org1138Estimation of errors in diffraction data measured by CCD area detectorshttp://scripts.iucr.org/cgi-bin/paper?ea5116
Current methods for diffraction-spot integration from CCD area detectors typically underestimate the errors in the measured intensities. In an attempt to understand fully and identify correctly the sources of all contributions to these errors, a simulation of a CCD-based area-detector module has been produced to address the problem of correct handling of data from such detectors. Using this simulation, it has been shown how, and by how much, measurement errors are underestimated. A model of the detector statistics is presented and an adapted summation integration routine that takes this into account is shown to result in more realistic error estimates. In addition, the effect of correlations between pixels on two-dimensional profile fitting is demonstrated and the problems surrounding improvements to profile-fitting algorithms are discussed. In practice, this requires knowledge of the expected correlation between pixels in the image.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Waterman, D.Evans, G.2010-10-01doi:10.1107/S0021889810033418International Union of CrystallographyA simulation of a CCD area detector is presented. The methods for error estimation on data obtained from images from such detectors by two-dimensional integration are considered and improvements incorporating a realistic instrumental response are suggested.enERROR ESTIMATION; CCD AREA DETECTORS; DETECTOR SIMULATION; PIXEL CORRELATIONCurrent methods for diffraction-spot integration from CCD area detectors typically underestimate the errors in the measured intensities. In an attempt to understand fully and identify correctly the sources of all contributions to these errors, a simulation of a CCD-based area-detector module has been produced to address the problem of correct handling of data from such detectors. Using this simulation, it has been shown how, and by how much, measurement errors are underestimated. A model of the detector statistics is presented and an adapted summation integration routine that takes this into account is shown to result in more realistic error estimates. In addition, the effect of correlations between pixels on two-dimensional profile fitting is demonstrated and the problems surrounding improvements to profile-fitting algorithms are discussed. In practice, this requires knowledge of the expected correlation between pixels in the image.text/htmlEstimation of errors in diffraction data measured by CCD area detectorstext6432010-10-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1356med@iucr.orgDecember 201013711600-5767Jmol – a paradigm shift in crystallographic visualizationhttp://scripts.iucr.org/cgi-bin/paper?kk5066
Recent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Hanson, R.M.2010-10-01doi:10.1107/S0021889810030256International Union of CrystallographyFeatures of Jmol that allow new ways for students to interact with three-dimensional virtual models and explore molecular and crystallographic symmetry are described.enCRYSTALLOGRAPHIC EDUCATION; SYMMETRY; VISUALIZATION SOFTWARE; JMOLRecent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.text/htmlJmol – a paradigm shift in crystallographic visualizationtext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1250med@iucr.org1260Teaching crystallography to undergraduate physical chemistry studentshttp://scripts.iucr.org/cgi-bin/paper?kk5059
Teaching goals, laboratory experiments and homework assignments are described for teaching crystallography as part of two undergraduate physical chemistry courses. A two-week teaching module is suggested for introductory physical chemistry, including six to eight classroom sessions, several laboratory experiences and a 3 h computer-based session, to acquaint undergraduate physical chemistry students with crystals, diffraction patterns, the mathematics of structure determination by X-ray diffraction, data collection, structure solution and the chemical insights available from crystal structure information. Student projects and laboratory work for three to four weeks of an advanced physical chemistry course are presented. Topics such as symmetry operators, space groups, systematic extinctions, methods of solving the phase problem, the Patterson map, anomalous scattering, synchrotron radiation, crystallographic refinement, hydrogen bonding and neutron diffraction all lead to the goal of understanding and evaluating a crystallographic journal article. Many of the ideas presented here could also be adapted for inorganic chemistry courses.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Pett, V.B.2010-10-01doi:10.1107/S0021889810028384International Union of CrystallographyClassroom demonstrations, laboratory experiments and homework assignments are suggested that will increase student interest and comprehension in both introductory and advanced physical chemistry courses.enCRYSTALLOGRAPHIC EDUCATION; TEACHING MATERIALSTeaching goals, laboratory experiments and homework assignments are described for teaching crystallography as part of two undergraduate physical chemistry courses. A two-week teaching module is suggested for introductory physical chemistry, including six to eight classroom sessions, several laboratory experiences and a 3 h computer-based session, to acquaint undergraduate physical chemistry students with crystals, diffraction patterns, the mathematics of structure determination by X-ray diffraction, data collection, structure solution and the chemical insights available from crystal structure information. Student projects and laboratory work for three to four weeks of an advanced physical chemistry course are presented. Topics such as symmetry operators, space groups, systematic extinctions, methods of solving the phase problem, the Patterson map, anomalous scattering, synchrotron radiation, crystallographic refinement, hydrogen bonding and neutron diffraction all lead to the goal of understanding and evaluating a crystallographic journal article. Many of the ideas presented here could also be adapted for inorganic chemistry courses.text/htmlTeaching crystallography to undergraduate physical chemistry studentstext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1139med@iucr.org1143Update on the tutorial for learning and teaching macromolecular crystallographyhttp://scripts.iucr.org/cgi-bin/paper?kk5070
Two new experiments (single isomorphous replacement including anomalous-scattering effects and radiation damage-induced phasing) have been designed to complement the five experiments (sulfur single-wavelength anomalous diffraction, multiple-wavelength anomalous diffraction, molecular replacement, ion binding and ligand binding) of the first edition of the previously described tutorial for learning and teaching macromolecular crystallography [Faust, Panjikar, Mueller, Parthasarathy, Schmidt, Lamzin & Weiss (2008). J. Appl. Cryst. 41, 1161–1172]. Furthermore, the tutorial has been re-organized and in part re-written to reflect the comments and suggestions of users. The most significant overhaul was applied to the data-processing part of the tutorial. Nevertheless, the convenient features that all of the utilized proteins used are commercially available and that they can be easily and reproducibly crystallized and mounted for diffraction data collection have been retained. Also, for all of the seven experiments the raw diffraction images and the processed data are provided for illustrating and teaching the steps of data processing and structure determination.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Faust, A.Puehringer, S.Darowski, N.Panjikar, S.Diederichs, K.Mueller, U.Weiss, M.S.2010-10-01doi:10.1107/S0021889810028189International Union of CrystallographyThe previously described macromolecular crystallography tutorial [Faust, Panjikar, Mueller, Parthasarathy, Schmidt, Lamzin & Weiss (2008). J. Appl. Cryst. 41, 1161–1172] has been significantly revised and expanded with two more experiments.enCRYSTALLOGRAPHIC EDUCATION; SIRAS; RIP; SULFUR SIR; MIR; MOLECULAR REPLACEMENT; ION BINDING; LIGAND BINDING; DATA PROCESSING; STRUCTURE DETERMINATIONTwo new experiments (single isomorphous replacement including anomalous-scattering effects and radiation damage-induced phasing) have been designed to complement the five experiments (sulfur single-wavelength anomalous diffraction, multiple-wavelength anomalous diffraction, molecular replacement, ion binding and ligand binding) of the first edition of the previously described tutorial for learning and teaching macromolecular crystallography [Faust, Panjikar, Mueller, Parthasarathy, Schmidt, Lamzin & Weiss (2008). J. Appl. Cryst. 41, 1161–1172]. Furthermore, the tutorial has been re-organized and in part re-written to reflect the comments and suggestions of users. The most significant overhaul was applied to the data-processing part of the tutorial. Nevertheless, the convenient features that all of the utilized proteins used are commercially available and that they can be easily and reproducibly crystallized and mounted for diffraction data collection have been retained. Also, for all of the seven experiments the raw diffraction images and the processed data are provided for illustrating and teaching the steps of data processing and structure determination.text/htmlUpdate on the tutorial for learning and teaching macromolecular crystallographytext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1230med@iucr.org1237Teaching general chemistry, solid-state chemistry and crystallography in one comprehensive undergraduate course: can the effect be synergistic?http://scripts.iucr.org/cgi-bin/paper?kk5073
This contribution describes a 30-year experience of teaching a general course in solid-state chemistry for undergraduates, which introduces at the same time the main concepts of crystallography, gives an introduction to structure analysis techniques, and makes links to courses in inorganic chemistry, organic chemistry and biochemistry. Such a combination can be beneficial for bringing the fundamentals of crystallography (basics and techniques) closer to its `users' – chemists, materials scientists, biologists – and can be considered as an attempt to create a course in `applied crystallography'. The aim of the course is to teach chemists which chemical information can be retrieved from a crystal structure and how. This is complementary to more generally accepted courses, which teach how to obtain structural information and to describe crystal structures.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Boldyreva, E.2010-10-01doi:10.1107/S0021889810027780International Union of CrystallographyThis contribution describes a 30-year experience of teaching a general course in solid-state chemistry for undergraduates, which introduces at the same time the main concepts of crystallography, gives an introduction into structure analysis techniques and makes links to courses in inorganic chemistry, organic chemistry and biochemistry.enCRYSTALLOGRAPHIC EDUCATION; SOLID-STATE CHEMISTRY; MATERIALS SCIENCE; GENERAL CHEMISTRY; ORGANIC CHEMISTRY; INTERMOLECULAR INTERACTIONS; ELECTRONIC STRUCTURE; STRUCTURE-PROPERTIES RELATIONSHIPSThis contribution describes a 30-year experience of teaching a general course in solid-state chemistry for undergraduates, which introduces at the same time the main concepts of crystallography, gives an introduction to structure analysis techniques, and makes links to courses in inorganic chemistry, organic chemistry and biochemistry. Such a combination can be beneficial for bringing the fundamentals of crystallography (basics and techniques) closer to its `users' – chemists, materials scientists, biologists – and can be considered as an attempt to create a course in `applied crystallography'. The aim of the course is to teach chemists which chemical information can be retrieved from a crystal structure and how. This is complementary to more generally accepted courses, which teach how to obtain structural information and to describe crystal structures.text/htmlTeaching general chemistry, solid-state chemistry and crystallography in one comprehensive undergraduate course: can the effect be synergistic?text52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1172med@iucr.org1180Crystal cookery – using high-throughput technologies and the grocery store as a teaching toolhttp://scripts.iucr.org/cgi-bin/paper?kk5077
Crystallography is a multidisciplinary field that links divergent areas of mathematics, science and engineering to provide knowledge of life on an atomic scale. Crystal growth, a key component of the field, is an ideal vehicle for education. Crystallization has been used with a `grocery store chemistry' approach and linked to high-throughput remote-access screening technologies. This approach provides an educational opportunity that can effectively teach the scientific method, readily accommodate different levels of educational experience, and reach any student with access to a grocery store, a post office and the internet. This paper describes the formation of the program through the students who helped develop and prototype the procedures. A summary is presented of the analysis and preliminary results and a description given of how the program could be linked with other aspects of crystallography. This approach has the potential to bridge the gap between students in remote locations and with limited funding, and access to scientific resources, providing students with an international-level research experience.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Luft, J.R.Furlani, N.M.NeMoyer, R.E.Penna, E.J.Wolfley, J.R.Snell, M.E.Potter, S.A.Snell, E.H.2010-10-01doi:10.1107/S0021889810027640International Union of CrystallographyUsing high-throughput crystallization screening technologies and data analysis, an educational program has been developed to teach the scientific method through crystallization and access to a grocery store, a post office and the internet.enCRYSTALLOGRAPHIC EDUCATION; HIGH THROUGHPUTCrystallography is a multidisciplinary field that links divergent areas of mathematics, science and engineering to provide knowledge of life on an atomic scale. Crystal growth, a key component of the field, is an ideal vehicle for education. Crystallization has been used with a `grocery store chemistry' approach and linked to high-throughput remote-access screening technologies. This approach provides an educational opportunity that can effectively teach the scientific method, readily accommodate different levels of educational experience, and reach any student with access to a grocery store, a post office and the internet. This paper describes the formation of the program through the students who helped develop and prototype the procedures. A summary is presented of the analysis and preliminary results and a description given of how the program could be linked with other aspects of crystallography. This approach has the potential to bridge the gap between students in remote locations and with limited funding, and access to scientific resources, providing students with an international-level research experience.text/htmlCrystal cookery – using high-throughput technologies and the grocery store as a teaching tooltext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1189med@iucr.org1207Pushing the boundaries of technology to educate and train the next generation of crystallographershttp://scripts.iucr.org/cgi-bin/paper?kk5068
This article describes the evolution of educational technologies, moving from the Web 1.0 to the current Web 3.0 decade, with the aim of stimulating discussion and inspiring innovative and effective crystallography education in the Web 3.0 decade. In the last 15 years, academic crystallography has largely migrated from a research specialty to a technique employed by a broad user community. This has led to the growth of and dependence on independently funded workshops and summer schools, as well as other non-traditional curricular resources for crystallography instruction, such as web pages and online courses, which allow crystallography to be self-taught. In fact, informal courses and e-learning constitute 70–80% of all learning today, and students expect on-demand learning. Implementing modern web technologies with sound pedagogy requires skilful integration of relevant, often disparate, resources into useful and usable frameworks, enabling learners to interact, explore new situations, and use scientific reasoning skills such as hypothesis testing and model-based reasoning. The evident disproportion in implementing contemporary technologies into our global crystallography education resources requires that we shift our focus from simply imparting subject knowledge by posting largely text-based content to empowering students with the fundamental processes and skills needed for on-demand learning and practice in crystallography.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Kantardjieff, K.2010-10-01doi:10.1107/S0021889810027494International Union of CrystallographyThe science of crystallography has always pushed the boundaries of technology, and the time is now ripe to push them again, not just to advance our research capabilities, but to attract and train the next generation.enWEB 2.0; WEB 3.0; CRYSTALLOGRAPHIC EDUCATION; EDUCATIONAL TECHNOLOGY; CYBERINFRASTRUCTURE; E-LEARNINGThis article describes the evolution of educational technologies, moving from the Web 1.0 to the current Web 3.0 decade, with the aim of stimulating discussion and inspiring innovative and effective crystallography education in the Web 3.0 decade. In the last 15 years, academic crystallography has largely migrated from a research specialty to a technique employed by a broad user community. This has led to the growth of and dependence on independently funded workshops and summer schools, as well as other non-traditional curricular resources for crystallography instruction, such as web pages and online courses, which allow crystallography to be self-taught. In fact, informal courses and e-learning constitute 70–80% of all learning today, and students expect on-demand learning. Implementing modern web technologies with sound pedagogy requires skilful integration of relevant, often disparate, resources into useful and usable frameworks, enabling learners to interact, explore new situations, and use scientific reasoning skills such as hypothesis testing and model-based reasoning. The evident disproportion in implementing contemporary technologies into our global crystallography education resources requires that we shift our focus from simply imparting subject knowledge by posting largely text-based content to empowering students with the fundamental processes and skills needed for on-demand learning and practice in crystallography.text/htmlPushing the boundaries of technology to educate and train the next generation of crystallographerstext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1276med@iucr.org1282Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization systemhttp://scripts.iucr.org/cgi-bin/paper?kk5065
The Microcapillary Protein Crystallization System (MPCS) is a microfluidic, plug-based crystallization technology that generates X-ray diffraction-ready protein crystals in nanolitre volumes. In this study, 28 out of 29 (93%) proteins crystallized by traditional vapor diffusion experiments were successfully crystallized by chemical gradient optimization experiments using the MPCS technology. In total, 90 out of 120 (75%) protein/precipitant combinations leading to initial crystal hits from vapor diffusion experiments were successfully crystallized using MPCS technology. Many of the resulting crystals produced high-quality X-ray diffraction data, and six novel protein structures that were derived from crystals harvested from MPCS CrystalCards are reported.http://creativecommons.org/licenses/by/2.0/ukurn:issn:0021-8898Gerdts, C.J.Stahl, G.L.Napuli, A.Staker, B.Abendroth, J.Edwards, T.E.Myler, P.Van Voorhis, W.Nollert, P.Stewart, L.J.2010-10-01doi:10.1107/S0021889810027378International Union of CrystallographyThe Microcapillary Protein Crystallization System (MPCS) is used to successfully optimize protein crystals from 28 out of 29 tested proteins. Six protein structures have been determined from diffraction-ready crystals grown inside and harvested directly from the MPCS CrystalCards, which are compatible with the recently commercialized and automated MPCS Plug Maker instrument.enPROTEIN CRYSTALS; MICROFLUIDS; PLUGS; GENOMICSThe Microcapillary Protein Crystallization System (MPCS) is a microfluidic, plug-based crystallization technology that generates X-ray diffraction-ready protein crystals in nanolitre volumes. In this study, 28 out of 29 (93%) proteins crystallized by traditional vapor diffusion experiments were successfully crystallized by chemical gradient optimization experiments using the MPCS technology. In total, 90 out of 120 (75%) protein/precipitant combinations leading to initial crystal hits from vapor diffusion experiments were successfully crystallized using MPCS technology. Many of the resulting crystals produced high-quality X-ray diffraction data, and six novel protein structures that were derived from crystals harvested from MPCS CrystalCards are reported.text/htmlNanovolume optimization of protein crystal growth using the microcapillary protein crystallization systemtext51432010-10-01Journal of Applied Crystallographyhttp://creativecommons.org/licenses/by/2.0/uk0021-8898research papers1078med@iucr.org10831600-5767Scientific inquiry, inference and critical reasoning in the macromolecular crystallography curriculumhttp://scripts.iucr.org/cgi-bin/paper?kk5067
The astounding progress in methods and technology that led to the undisputed success and impact of biomolecular crystallography on areas ranging from essential structural biology to therapeutic drug discovery or the study of molecular complexes of ever increasing size and beauty has brought with it new requirements for the education of students in the field. With the great power of modern crystallography comes great responsibility for its appropriate use, and a modern curriculum must extend beyond the delivery of required technical expertise. The complexity of macromolecular models and the sometimes low determinacy, combined with local variety in structure quality, requires that the student is provided with means of critical analysis and hypothesis testing that extend beyond classical validation, developing a mindset that remains robust against mental bias towards finding what one seeks. The increasing neglect of critical analysis and hypothesis testing in many undergraduate curricula requires that the modern crystallography curriculum itself addresses such fundamental analytical tools of the scientific method to avoid high-profile structure retractions that might tarnish the otherwise unrivalled contributions of macromol­ecular crystallography to our understanding of the molecular basis of life.Copyright (c) 2010 International Union of Crystallographyurn:issn:0021-8898Rupp, B.2010-10-01doi:10.1107/S0021889810027184International Union of CrystallographyAn essay on the importance of incorporating basic scientific reasoning and common sense into the biomolecular crystallography curriculum to safeguard against mistakes and self-deception in the interpretation of macromolecular structure models is presented.enMODEL INTERPRETATION; BAYESIAN INFERENCE; VALIDATION; SCIENTIFIC REASONING; KUHN; POPPER; FEYERABENDThe astounding progress in methods and technology that led to the undisputed success and impact of biomolecular crystallography on areas ranging from essential structural biology to therapeutic drug discovery or the study of molecular complexes of ever increasing size and beauty has brought with it new requirements for the education of students in the field. With the great power of modern crystallography comes great responsibility for its appropriate use, and a modern curriculum must extend beyond the delivery of required technical expertise. The complexity of macromolecular models and the sometimes low determinacy, combined with local variety in structure quality, requires that the student is provided with means of critical analysis and hypothesis testing that extend beyond classical validation, developing a mindset that remains robust against mental bias towards finding what one seeks. The increasing neglect of critical analysis and hypothesis testing in many undergraduate curricula requires that the modern crystallography curriculum itself addresses such fundamental analytical tools of the scientific method to avoid high-profile structure retractions that might tarnish the otherwise unrivalled contributions of macromol­ecular crystallography to our understanding of the molecular basis of life.text/htmlScientific inquiry, inference and critical reasoning in the macromolecular crystallography curriculumtext52432010-10-01Journal of Applied CrystallographyCopyright (c) 2010 International Union of Crystallography0021-8898research papers1242med@iucr.org1249How to read (and understand) Volume A of International Tables for Crystallography: an introduction for nonspecialistshttp://scripts.iucr.org/cgi-bin/paper?kk5061
Since fewer and fewer students get proper crystallographic education at the undergraduate level, the responsibility to promote and propagate this knowledge must be directed to alternative channels. It is not a marginal issue, because the language of crystallography is rather hermetic and, without proper support, it might disappear from the collective scientific knowledge, so that in the next generation there would be no-one able to use it properly, to say nothing about advancing the field. Black-box crystallography might be useful in some situations, but it cannot replace well informed, conscious scientific pursuits by properly trained specialists. Without sufficient understanding of crystallographic terms and principles, the now thriving branch of structural research would wither, and this could have particularly lamentable consequences for structural biology. The purpose of this article is to teach non-initiated persons, primarily structural biologists, how to interpret the information contained in the fundamental Volume A of International Tables for Crystallography (ITA). An excellent and comprehensive overview of many issues concerning crystal symmetry is presented in a book by Burns & Glazer (Space Groups for Solid State Scientists, 2nd ed. New York: Academic Press, 1990), also explaining the contents of ITA, but this text is unfortunately not popular among structural biologists. There are several superb handbooks explaining the foundations of structural crystallography but they usual